diff --git a/README.md b/README.md index 82f15ec..c6337a8 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![Continuous Integration](https://github.com/bihealth/varfish-annotator/actions/workflows/ci.yml/badge.svg)](https://github.com/bihealth/varfish-annotator/actions?query=workflow%3Acontinuous-integration) [![Coverage Status](https://coveralls.io/repos/github/bihealth/varfish-annotator/badge.svg?branch=main)](https://coveralls.io/github/bihealth/varfish-annotator?branch=main) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/varfish-annotator-cli/README.html) # VarFish Annotator @@ -174,3 +175,15 @@ The folder `/tests` contains some data sets that are appropriate for system (aka You can build the data sets with the `build.sh` script that is available in each folder. This script also serves for documenting the test data's provenance. The Jannovar software must be available as `jannovar` (e.g., through bioconda) on your `PATH` and you will need `samtools`. + +## Using JDK >=18 + +The **tests** use [junit5-system-exit](https://github.com/tginsberg/junit5-system-exit) for detecting `System.exit()` calls. +In JDK 18 you have to use the `-Djava.security.manager=allow` flag. +Issue [tginsberg/junit5-system-exit#10](https://github.com/tginsberg/junit5-system-exit/issues/10) tracks this issue. + +## Developing on Windows + +There is an issue with removing temporary directories on Windows. +Apparently, HTSJDK does not properly close files. +Set `-Djunit.jupiter.tempdir.cleanup.mode.default=NEVER` to work around this issue. \ No newline at end of file diff --git a/pom.xml b/pom.xml index 05a3ee8..ca3d41d 100644 --- a/pom.xml +++ b/pom.xml @@ -14,9 +14,8 @@ UTF-8 1.3 - 5.7.2 - 1.7.2 - 30.0-jre + 5.9.0 + 31.1-jre 2.5.1 7 1.7.24 diff --git a/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected b/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected index 2625866..6ae69bc 100644 --- a/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected +++ b/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected @@ -1,2 +1,2 @@ release chromosome chromosome_no bin chromosome2 chromosome_no2 bin2 pe_orientation start end start_ci_left start_ci_right end_ci_left end_ci_right case_id set_id sv_uuid caller sv_type sv_sub_type info num_hom_alt num_hom_ref num_het num_hemi_alt num_hemi_ref genotype -GRCh37 22 22 89 22 22 89 3to5 17400000 17700000 -29 29 -29 29 . . UUID EMBL.DELLYv1.1.3 DEL DEL {"""backgroundCarriers""":0,"""affectedCarriers""":0,"""unaffectedCarriers""":0} 0 2 1 0 0 {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ft""":{"""LowQual"""},"""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4,"""cn""":2},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":35,"""pec""":0,"""pev""":0,"""src""":29,"""srv""":2,"""cn""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":67,"""pec""":0,"""pev""":0,"""src""":32,"""srv""":1,"""cn""":2}} +GRCh37 22 22 89 22 22 89 3to5 17400000 17700000 -29 29 -29 29 . . UUID EMBL.DELLYv1.1.3 DEL DEL {"""affectedCarriers""":0,"""backgroundCarriers""":0,"""unaffectedCarriers""":0} 0 2 1 0 0 {"""Case_1_father-N1-DNA1-WGS1""":{"""cn""":2,"""ft""":{"""LowQual"""},"""gq""":14,"""gt""":"""0/1""","""pec""":0,"""pev""":0,"""src""":34,"""srv""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":35,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":29,"""srv""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":67,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":32,"""srv""":1}} diff --git a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java index c5c88a6..941f043 100644 --- a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java +++ b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java @@ -247,7 +247,11 @@ private void annotateSvVcf( // Write out header. try { - gtWriter.append(Joiner.on("\t").join(gtRecordBuilder.getHeaders()) + "\n"); + gtWriter.append( + GenotypeRecord.tsvHeader( + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS), + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS)) + + "\n"); // Write feature-effects header. featureEffectsWriter.append(Joiner.on("\t").join(HEADERS_FEATURE_EFFECTS) + "\n"); } catch (IOException e) { @@ -481,10 +485,14 @@ private void annotateVariantContext( } // Write out record with the genotype. - final List gtOutRec = + final GenotypeRecord gtOutRec = gtRecordBuilder.buildRecord(variantId, svGenomeVar, ctx, genomeVersion, i); try { - gtWriter.append(Joiner.on("\t").useForNull(".").join(gtOutRec) + "\n"); + gtWriter.append( + gtOutRec.toTsv( + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS), + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS)) + + "\n"); } catch (IOException e) { throw new VarfishAnnotatorException("Problem writing to genotypes call file.", e); } diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf37Chr1Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf37Chr1Test.java index 9832306..26605d9 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf37Chr1Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf37Chr1Test.java @@ -103,8 +103,11 @@ void runTest( } } else { Assertions.assertEquals( - expectedDbInfos, FileUtils.readFileToString(outputDbInfoPath, "utf-8")); - Assertions.assertEquals(expectedGts, FileUtils.readFileToString(outputGtsPath, "utf-8")); + expectedDbInfos, + FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n")); + Assertions.assertEquals( + expectedGts, + FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n")); } } diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf38Chr1Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf38Chr1Test.java index d9248c5..9664263 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf38Chr1Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf38Chr1Test.java @@ -96,8 +96,11 @@ void runTest( } } else { Assertions.assertEquals( - expectedDbInfos, FileUtils.readFileToString(outputDbInfoPath, "utf-8")); - Assertions.assertEquals(expectedGts, FileUtils.readFileToString(outputGtsPath, "utf-8")); + expectedDbInfos, + FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n")); + Assertions.assertEquals( + expectedGts, + FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n")); } } diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/RunWithRealWorldData37Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/RunWithRealWorldData37Test.java index 2e85989..c97e889 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/RunWithRealWorldData37Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/RunWithRealWorldData37Test.java @@ -103,11 +103,11 @@ void runTest( } } else { Assertions.assertEquals( - FileUtils.readFileToString(expectedDbInfosPath, "utf-8"), - FileUtils.readFileToString(outputDbInfoPath, "utf-8")); + FileUtils.readFileToString(expectedDbInfosPath, "utf-8").replaceAll("\\r\\n?", "\n"), + FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n")); Assertions.assertEquals( - FileUtils.readFileToString(expectedGtsPath, "utf-8"), - FileUtils.readFileToString(outputGtsPath, "utf-8")); + FileUtils.readFileToString(expectedGtsPath, "utf-8").replaceAll("\\r\\n?", "\n"), + FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n")); } } diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java index 0bcb82c..c16ddc1 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java @@ -117,10 +117,14 @@ void runTest( } } else { Assertions.assertEquals( - expectedDbInfos, FileUtils.readFileToString(outputDbInfoPath, "utf-8")); - Assertions.assertEquals(expectedGts, FileUtils.readFileToString(outputGtsPath, "utf-8")); + expectedDbInfos, + FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n")); Assertions.assertEquals( - expectedFeatureEffects, FileUtils.readFileToString(outputFeatureEffects, "utf-8")); + expectedGts, + FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n")); + Assertions.assertEquals( + expectedFeatureEffects, + FileUtils.readFileToString(outputFeatureEffects, "utf-8").replaceAll("\\r\\n?", "\n")); } } @@ -138,11 +142,11 @@ void testWithSingleton(boolean gzipOutput) throws IOException { + "GRCh37\tthousand_genomes\tv5b.20130502\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\", \"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" - + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" - + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; + + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" + + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" + + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( @@ -172,11 +176,11 @@ void testWithTrio(boolean gzipOutput) throws IOException { + "GRCh37\tthousand_genomes\tv5b.20130502\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\"},\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":57,\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":39,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\", \"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":157,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n" - + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\", \"\"\"MAX_PE_COUNT\"\"\", \"\"\"MAX_SR_AAF\"\"\", \"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n" - + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\", \"\"\"MAX_PE_COUNT\"\"\", \"\"\"MAX_SR_AAF\"\"\", \"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"; + + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\"},\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":57,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":157,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n" + + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n" + + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( @@ -226,8 +230,8 @@ void testAnnotateHemiMale() throws Exception { + "GRCh37\tthousand_genomes\tv5b.20130502\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh37\tX\t23\t592\tX\t23\t592\t3to5\t1000000\t1001000\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\tX\t23\t607\tX\t23\t607\t5to3\t3000000\t3001000\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t0\t1\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; + + "GRCh37\tX\t23\t592\tX\t23\t592\t3to5\t1000000\t1001000\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\tX\t23\t607\tX\t23\t607\t5to3\t3000000\t3001000\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t0\t1\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( @@ -256,8 +260,8 @@ void testAnnotateHemiFamily() throws Exception { + "GRCh37\tthousand_genomes\tv5b.20130502\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh37\tX\t23\t592\tX\t23\t592\t3to5\t1000000\t1001000\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t1\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\"},\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":57,\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\tX\t23\t607\tX\t23\t607\t5to3\t3000000\t3001000\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t2\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":39,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; + + "GRCh37\tX\t23\t592\tX\t23\t592\t3to5\t1000000\t1001000\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t1\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\"},\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":57,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\tX\t23\t607\tX\t23\t607\t5to3\t3000000\t3001000\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t2\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( @@ -286,11 +290,11 @@ void testWithSingletonOptOutChrom2() throws IOException { + "GRCh37\tthousand_genomes\tv5b.20130502\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh37\t1\t1\t599\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t604\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t780\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\", \"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" - + "GRCh37\t14\t14\t1299\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" - + "GRCh37\t1\t1\t654\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; + + "GRCh37\t1\t1\t599\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t604\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t780\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" + + "GRCh37\t14\t14\t1299\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" + + "GRCh37\t1\t1\t654\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( @@ -319,11 +323,11 @@ void testWithSingletonOptOutDbCounts() throws IOException { + "GRCh37\tthousand_genomes\tv5b.20130502\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tgenotype\n" - + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\", \"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" - + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" - + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; + + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" + + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" + + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( @@ -352,8 +356,8 @@ void testWithSingletonBnd() throws IOException { + "GRCh37\tthousand_genomes\tv5b.20130502\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh37\t2\t2\t585\t1\t1\t585\t3to5\t10265\t10265\t-248\t248\t-248\t248\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.1\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":249239891,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":23,\"\"\"pec\"\"\":10,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh37\t1\t1\t2486\t2\t2\t2486\t5to3\t249239891\t249239891\t-248\t248\t-248\t248\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.1\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"2\"\"\",\"\"\"pos2\"\"\":10265,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":23,\"\"\"pec\"\"\":10,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; + + "GRCh37\t2\t2\t585\t1\t1\t585\t3to5\t10265\t10265\t-248\t248\t-248\t248\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.1\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":249239891,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":23,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":10,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t2486\t2\t2\t2486\t5to3\t249239891\t249239891\t-248\t248\t-248\t248\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.1\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"2\"\"\",\"\"\"pos2\"\"\":10265,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":23,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":10,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr22Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr22Test.java index 5e9fd6d..c97ef80 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr22Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr22Test.java @@ -115,10 +115,14 @@ void runTest( } } else { Assertions.assertEquals( - expectedDbInfos, FileUtils.readFileToString(outputDbInfoPath, "utf-8")); - Assertions.assertEquals(expectedGts, FileUtils.readFileToString(outputGtsPath, "utf-8")); + expectedDbInfos, + FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n")); Assertions.assertEquals( - expectedFeatureEffects, FileUtils.readFileToString(outputFeatureEffects, "utf-8")); + expectedGts, + FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n")); + Assertions.assertEquals( + expectedFeatureEffects, + FileUtils.readFileToString(outputFeatureEffects, "utf-8").replaceAll("\\r\\n?", "\n")); } } @@ -138,7 +142,7 @@ void testWithTrio(boolean gzipOutput) throws IOException { + "GRCh37\tvarfish-annotator-db\tfor-testing\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh37\t22\t22\t89\t22\t22\t89\t3to5\t17400000\t17700000\t-29\t29\t-29\t29\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv1.1.3\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"Case_1_father-N1-DNA1-WGS1\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"LowQual\"\"\"},\"\"\"gq\"\"\":14,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":34,\"\"\"srv\"\"\":4,\"\"\"cn\"\"\":2},\"\"\"Case_1_index-N1-DNA1-WGS1\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":35,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":29,\"\"\"srv\"\"\":2,\"\"\"cn\"\"\":2},\"\"\"Case_1_mother-N1-DNA1-WGS1\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":67,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":32,\"\"\"srv\"\"\":1,\"\"\"cn\"\"\":2}}\n"; + + "GRCh37\t22\t22\t89\t22\t22\t89\t3to5\t17400000\t17700000\t-29\t29\t-29\t29\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv1.1.3\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"Case_1_father-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"ft\"\"\":{\"\"\"LowQual\"\"\"},\"\"\"gq\"\"\":14,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":34,\"\"\"srv\"\"\":4},\"\"\"Case_1_index-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"gq\"\"\":35,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":29,\"\"\"srv\"\"\":2},\"\"\"Case_1_mother-N1-DNA1-WGS1\"\"\":{\"\"\"cn\"\"\":2,\"\"\"gq\"\"\":67,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":32,\"\"\"srv\"\"\":1}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n" + ".\t.\t00000000-0000-0000-0000-000000000000\t51816\tNM_017424.2\tTRUE\t{\"transcript_ablation\",\"coding_transcript_variant\"}\tENSG00000093072\tENST00000262607.3\tTRUE\t{\"transcript_ablation\",\"coding_transcript_variant\"}\n" diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf38Chr1Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf38Chr1Test.java index 6e5348d..4394cef 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf38Chr1Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf38Chr1Test.java @@ -94,10 +94,14 @@ void runTest( } } else { Assertions.assertEquals( - expectedDbInfos, FileUtils.readFileToString(outputDbInfoPath, "utf-8")); - Assertions.assertEquals(expectedGts, FileUtils.readFileToString(outputGtsPath, "utf-8")); + expectedDbInfos, + FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n")); Assertions.assertEquals( - expectedFeatureEffects, FileUtils.readFileToString(outputFeatureEffects, "utf-8")); + expectedGts, + FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n")); + Assertions.assertEquals( + expectedFeatureEffects, + FileUtils.readFileToString(outputFeatureEffects, "utf-8").replaceAll("\\r\\n?", "\n")); } } @@ -113,11 +117,11 @@ void testWithSingleton(boolean gzipOutput) throws IOException { + "GRCh38\thgmd_public\tensembl_r104\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\", \"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" - + "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" - + "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; + + "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7}}\n" + + "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" + + "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( @@ -142,11 +146,11 @@ void testWithTrio(boolean gzipOutput) throws IOException { + "GRCh38\thgmd_public\tensembl_r104\n"; final String expectedGts = "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n" - + "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\"},\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":57,\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":39,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" - + "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\", \"\"\"MIN_PE_COUNT\"\"\", \"\"\"MIN_SR_AAF\"\"\", \"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":157,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n" - + "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\", \"\"\"MAX_PE_COUNT\"\"\", \"\"\"MAX_SR_AAF\"\"\", \"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n" - + "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\", \"\"\"MAX_PE_COUNT\"\"\", \"\"\"MAX_SR_AAF\"\"\", \"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"; + + "GRCh38\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\"},\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":57,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh38\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"ft\"\"\":{\"\"\"MIN_PE_AAF\"\"\",\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"},\"\"\"gq\"\"\":123,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gq\"\"\":157,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n" + + "GRCh38\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n" + + "GRCh38\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gq\"\"\":93,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"ft\"\"\":{\"\"\"MAX_PE_AAF\"\"\",\"\"\"MAX_PE_COUNT\"\"\",\"\"\"MAX_SR_AAF\"\"\",\"\"\"MAX_SR_COUNT\"\"\"},\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"; final String expectedFeatureEffects = "case_id\tset_id\tsv_uuid\trefseq_gene_id\trefseq_transcript_id\trefseq_transcript_coding\trefseq_effect\tensembl_gene_id\tensembl_transcript_id\tensembl_transcript_coding\tensembl_effect\n"; runTest( diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/RunWithRealWorldData37Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/RunWithRealWorldData37Test.java index 950c0ba..1692604 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/RunWithRealWorldData37Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/RunWithRealWorldData37Test.java @@ -111,14 +111,16 @@ void runTest( } } else { Assertions.assertEquals( - FileUtils.readFileToString(expectedDbInfosPath, "utf-8"), - FileUtils.readFileToString(outputDbInfoPath, "utf-8")); + FileUtils.readFileToString(expectedDbInfosPath, "utf-8").replaceAll("\\r\\n?", "\n"), + FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n")); Assertions.assertEquals( - FileUtils.readFileToString(expectedGtsPath, "utf-8"), - FileUtils.readFileToString(outputGtsPath, "utf-8")); + FileUtils.readFileToString(expectedGtsPath, "utf-8").replaceAll("\\r\\n?", "\n"), + FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n")); Assertions.assertEquals( - FileUtils.readFileToString(expectedFeatureEffectsPath, "utf-8"), - FileUtils.readFileToString(outputFeatureEffectsPath, "utf-8")); + FileUtils.readFileToString(expectedFeatureEffectsPath, "utf-8") + .replaceAll("\\r\\n?", "\n"), + FileUtils.readFileToString(outputFeatureEffectsPath, "utf-8") + .replaceAll("\\r\\n?", "\n")); } } diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats37Chr1Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats37Chr1Test.java index 7476457..b591870 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats37Chr1Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats37Chr1Test.java @@ -35,7 +35,7 @@ void initEach() { @Test void testParseable() throws Exception { String text = - SystemLambda.tapSystemOut( + SystemLambda.tapSystemOutNormalized( () -> { VarfishAnnotatorCli.main( new String[] { @@ -69,7 +69,7 @@ void testParseable() throws Exception { @Test void testNonParseable() throws Exception { String text = - SystemLambda.tapSystemOut( + SystemLambda.tapSystemOutNormalized( () -> { VarfishAnnotatorCli.main( new String[] { diff --git a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats38Chr1Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats38Chr1Test.java index 0df6977..e5d36b9 100644 --- a/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats38Chr1Test.java +++ b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/dbstats/DbStats38Chr1Test.java @@ -35,7 +35,7 @@ void initEach() { @Test void testParseable() throws Exception { String text = - SystemLambda.tapSystemOut( + SystemLambda.tapSystemOutNormalized( () -> { VarfishAnnotatorCli.main( new String[] { @@ -63,7 +63,7 @@ void testParseable() throws Exception { @Test void testNonParseable() throws Exception { String text = - SystemLambda.tapSystemOut( + SystemLambda.tapSystemOutNormalized( () -> { VarfishAnnotatorCli.main( new String[] { diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz deleted file mode 120000 index cccdaca..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz new file mode 100644 index 0000000..ad85f22 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi deleted file mode 120000 index 20c4ade..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi new file mode 100644 index 0000000..47877b6 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv b/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv deleted file mode 120000 index 8c52c64..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/Clinvar.tsv \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv b/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv new file mode 100644 index 0000000..35ee730 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv @@ -0,0 +1 @@ +release chromosome start end bin reference alternative clinvar_version set_type variation_type symbols hgnc_ids vcv summary_clinvar_review_status_label summary_clinvar_pathogenicity_label summary_clinvar_pathogenicity summary_clinvar_gold_stars summary_paranoid_review_status_label summary_paranoid_pathogenicity_label summary_paranoid_pathogenicity summary_paranoid_gold_stars details diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv.gz deleted file mode 120000 index a9c711b..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/Clinvar.tsv.gz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv.gz new file mode 100644 index 0000000..05860b2 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/Clinvar.tsv.gz differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz deleted file mode 120000 index b8016d3..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz new file mode 100644 index 0000000..1817df5 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz.tbi deleted file mode 120000 index c61301b..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz.tbi \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz.tbi new file mode 100644 index 0000000..1c6c70d Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/ExAC.r1.sites.vep.vcf.gz.tbi differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/HgmdPublicLocus.tsv.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/HgmdPublicLocus.tsv.gz deleted file mode 120000 index 5bb43f6..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/HgmdPublicLocus.tsv.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/HgmdPublicLocus.tsv.gz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/HgmdPublicLocus.tsv.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/HgmdPublicLocus.tsv.gz new file mode 100644 index 0000000..d2731f7 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/HgmdPublicLocus.tsv.gz differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/build.sh b/varfish-annotator-cli/src/test/resources/grch37-chr22/build.sh deleted file mode 120000 index 8a2f50f..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/build.sh +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/build.sh \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/build.sh b/varfish-annotator-cli/src/test/resources/grch37-chr22/build.sh new file mode 100755 index 0000000..fd0ec10 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/grch37-chr22/build.sh @@ -0,0 +1,122 @@ +#!/usr/bin/bash + +set -euo pipefail +set -x + +if [[ ! -e chr22.fa ]]; then + wget -O chr22.fa.gz.tmp https://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/chr22.fa.gz + zcat chr22.fa.gz.tmp >chr22.fa.tmp + mv chr22.fa.tmp chr22.fa +fi + +if [[ ! -e chr22_part.fa.fai ]]; then + samtools faidx chr22.fa chr22:1-22,000,000 > chr22_part.fa.tmp + perl -p -i -e 's/^>chr.*/>22/g' chr22_part.fa.tmp + gzip -c chr22_part.fa.tmp >chr22_part.fa.gz + mv chr22_part.fa.tmp chr22_part.fa + samtools faidx chr22_part.fa +fi + +# ADA2(hg19): 22:17,660,192-17,680,545 +# GAB4(hg19): 22:17,442,827-17,489,112 + +if [[ ! -e hg19_refseq.ser ]]; then + jannovar -Xmx4096m download -d hg19/ensembl --gene-ids ENSG00000093072 ENSG00000215568 # ADA2 GAB4 + cp data/hg19_refseq.ser hg19_refseq.ser.tmp + mv hg19_refseq.ser.tmp hg19_refseq.ser +fi + +if [[ ! -e hg19_ensembl.ser ]]; then + jannovar -Xmx4096m download -d hg19/ensembl --gene-ids 51816 128954 # ADA2 GAB4 + cp data/hg19_ensembl.ser hg19_ensembl.ser.tmp + mv hg19_ensembl.ser.tmp hg19_ensembl.ser +fi + +REGIONS="22:17,660,192-17,680,545 22:17,442,827-17,489,112" +BASEDIR=/fast/groups/cubi/work/projects/2021-07-20_varfish-db-downloader-holtgrewe/varfish-db-downloader + +( \ + tabix --only-header $BASEDIR/GRCh37/ExAC/r1/download/ExAC.r1.sites.vep.vcf.gz $REGIONS; \ + tabix $BASEDIR/GRCh37/ExAC/r1/download/ExAC.r1.sites.vep.vcf.gz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> ExAC.r1.sites.vep.vcf.gz +tabix -f ExAC.r1.sites.vep.vcf.gz + +( \ + tabix --only-header $BASEDIR/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS; \ + tabix $BASEDIR/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz +tabix -f gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz + +( \ + tabix --only-header $BASEDIR/GRCh37/gnomAD_genomes/r2.1.1/download/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS; \ + tabix $BASEDIR/GRCh37/gnomAD_genomes/r2.1.1/download/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz +tabix -f gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz + +( \ + tabix --only-header $BASEDIR/GRCh37/thousand_genomes/phase3/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz; \ + tabix $BASEDIR/GRCh37/thousand_genomes/phase3/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz +tabix -f ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz + +(head -n 1 /tmp/Clinvar.tsv; tail -n +2 /tmp/Clinvar.tsv | sort -k2,2V -k3,3n -k4,4n) \ +| bgzip -c >/tmp/Clinvar.tsv.gz +tabix -S 1 -b 3 -e 4 -s 2 -f /tmp/Clinvar.tsv.gz +head -n 1 /tmp/Clinvar.tsv >Clinvar.tsv.tmp +tabix /tmp/Clinvar.tsv.gz $REGIONS \ +>>Clinvar.tsv.tmp +gzip Clinvar.tsv.tmp +mv Clinvar.tsv.tmp.gz Clinvar.tsv.gz + +(head -n 1 /tmp/HgmdPublicLocus.tsv; tail -n +2 /tmp/HgmdPublicLocus.tsv | sort -k2,2V -k3,3n -k4,4n) \ +| bgzip -c >/tmp/HgmdPublicLocus.tsv.gz +tabix -S 1 -b 3 -e 4 -s 2 -f /tmp/HgmdPublicLocus.tsv.gz +head -n 1 /tmp/HgmdPublicLocus.tsv >HgmdPublicLocus.tsv.tmp +tabix /tmp/HgmdPublicLocus.tsv.gz $REGIONS \ +>>HgmdPublicLocus.tsv.tmp +gzip HgmdPublicLocus.tsv.tmp +mv HgmdPublicLocus.tsv.tmp.gz HgmdPublicLocus.tsv.gz + +BASEDIR=/fast/groups/cubi/work/projects/2022-07-06_VarFish_Course_Data/snappy-processing/ +VCF=$BASEDIR/variant_calling/output/bwa.gatk_hc.Case_1_index-N1-DNA1-WGS1/out/bwa.gatk_hc.Case_1_index-N1-DNA1-WGS1.vcf.gz + +( \ + tabix --only-header $VCF $REGIONS; \ + tabix $VCF $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> Case_1_index.gatk_hc.vcf.gz +tabix -f Case_1_index.gatk_hc.vcf.gz + +VCF=$BASEDIR/wgs_sv_calling/output/bwa.delly2.Case_1_index-N1-DNA1-WGS1/out/bwa.delly2.Case_1_index-N1-DNA1-WGS1.vcf.gz + +( \ + tabix --only-header $VCF $REGIONS; \ + ( \ + cat Case_1_index.delly2.extra.vcf; \ + tabix $VCF $REGIONS; \ + ) \ + | sort -k1,1V -k2,2n \ + | uniq; \b +) \ +| bgzip -c \ +> Case_1_index.delly2.vcf.gz +tabix -f Case_1_index.delly2.vcf.gz diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.fai b/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.fai deleted file mode 120000 index 536a624..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.fai +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/chr22_part.fa.fai \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.fai b/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.fai new file mode 100644 index 0000000..7a82bca --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.fai @@ -0,0 +1 @@ +22 22000000 4 60 61 diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.gz deleted file mode 120000 index f07eed4..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/chr22_part.fa.gz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.gz b/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.gz new file mode 100644 index 0000000..8552c49 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/chr22_part.fa.gz differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/db-info.txt-expected b/varfish-annotator-cli/src/test/resources/grch37-chr22/db-info.txt-expected deleted file mode 120000 index e991c02..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/db-info.txt-expected +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/db-info.txt-expected \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/db-info.txt-expected b/varfish-annotator-cli/src/test/resources/grch37-chr22/db-info.txt-expected new file mode 100644 index 0000000..199d786 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/grch37-chr22/db-info.txt-expected @@ -0,0 +1,12 @@ +Table clinvar_var +TABLE RELEASE CHROM COUNT +clinvar_var GRCh37 22 124 +Table hgmd_locus +TABLE RELEASE CHROM COUNT +hgmd_locus GRCh37 22 11 +Table gnomad_exome_var +TABLE RELEASE CHROM COUNT +gnomad_exome_var GRCh37 22 1437 +Table gnomad_genome_var +TABLE RELEASE CHROM COUNT +gnomad_genome_var GRCh37 22 6072 diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz deleted file mode 120000 index 3830186..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz new file mode 100644 index 0000000..ea39800 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi deleted file mode 120000 index e4a4bb1..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi new file mode 100644 index 0000000..ee100cc Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz deleted file mode 120000 index 4231f65..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz new file mode 100644 index 0000000..df8038f Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi deleted file mode 120000 index 19fb0ef..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi new file mode 100644 index 0000000..e380e78 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_ensembl.ser b/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_ensembl.ser deleted file mode 120000 index 5101818..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_ensembl.ser +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/hg19_ensembl.ser \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_ensembl.ser b/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_ensembl.ser new file mode 100644 index 0000000..7559a12 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_ensembl.ser differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_refseq.ser b/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_refseq.ser deleted file mode 120000 index e3069aa..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_refseq.ser +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/hg19_refseq.ser \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_refseq.ser b/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_refseq.ser new file mode 100644 index 0000000..e275a13 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/grch37-chr22/hg19_refseq.ser differ diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/run-tests.sh b/varfish-annotator-cli/src/test/resources/grch37-chr22/run-tests.sh deleted file mode 120000 index cef1aff..0000000 --- a/varfish-annotator-cli/src/test/resources/grch37-chr22/run-tests.sh +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/hg19-chr22/run-tests.sh \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/grch37-chr22/run-tests.sh b/varfish-annotator-cli/src/test/resources/grch37-chr22/run-tests.sh new file mode 100755 index 0000000..4ff6392 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/grch37-chr22/run-tests.sh @@ -0,0 +1,104 @@ +#!/usr/bin/bash + +set -euo pipefail +set -x + +SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) +cd $SCRIPT_DIR + +JAR=$(ls ../../varfish-annotator-cli/target/varfish-annotator-cli-*.jar | grep -v sources | tail -n 1) +VERSION=$(basename $JAR .jar | cut -d - -f 4-) + +## prepare + +gzip -d -c chr22_part.fa.gz > chr22_part.fa + +## step 0: help + +java -jar $JAR --help >/tmp/the-output +test -s /tmp/the-output + +set +e +java -jar $JAR > /tmp/the-output +retcode=$? +set -e +test 1 -eq $retcode +test -s /tmp/the-output + +## step 1: init-db + +java -jar $JAR init-db \ + --release GRCh37 \ + --db-release-info varfish-annotator:main \ + --db-release-info varfish-annotator-db:for-testing \ + --db-path /tmp/out \ + \ + --ref-path chr22_part.fa \ + \ + --db-release-info exac:r1.0 \ + --exac-path ExAC.r1.sites.vep.vcf.gz \ + \ + --db-release-info thousand_genomes:v3.20101123 \ + --thousand-genomes-path ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz \ + \ + --db-release-info clinvar:for-testing \ + --clinvar-path Clinvar.tsv.gz \ + \ + --db-release-info gnomad_exomes:r2.1.1 \ + --gnomad-exomes-path gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz \ + \ + --db-release-info gnomad_genomes:r2.1.1 \ + --gnomad-genomes-path gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz \ + \ + --db-release-info hgmd_public:for-testing \ + --hgmd-public HgmdPublicLocus.tsv.gz + +## step 2: db-info + +java -jar $JAR db-stats --db-path /tmp/out.h2.db --parseable \ +> /tmp/db-info.txt +diff /tmp/db-info.txt db-info.txt-expected + +## step 3: annotate + +java -jar $JAR annotate \ + --release GRCh37 \ + --input-vcf Case_1_index.gatk_hc.vcf.gz \ + --output-gts /tmp/Case_1_index.gatk_hc.gts.tsv \ + --output-db-info /tmp/Case_1_index.gatk_hc.db-info.tsv \ + --ref-path chr22_part.fa \ + --refseq-ser-path hg19_refseq.ser \ + --ensembl-ser-path hg19_ensembl.ser \ + --db-path /tmp/out.h2.db \ + --self-test-chr22-only + +diff /tmp/Case_1_index.gatk_hc.gts.tsv Case_1_index.gatk_hc.gts.tsv-expected +perl -p -i -e "s/${VERSION}/VERSION/g" /tmp/Case_1_index.gatk_hc.db-info.tsv +diff /tmp/Case_1_index.gatk_hc.db-info.tsv Case_1_index.gatk_hc.db-info.tsv-expected + +## step 4: annotate-svs + +java -jar $JAR annotate-svs \ + --release GRCh37 \ + --input-vcf Case_1_index.delly2.vcf.gz \ + --output-gts /tmp/Case_1_index.delly2.gts.tsv \ + --output-feature-effects /tmp/Case_1_index.delly2.feature-effects.tsv \ + --output-db-info /tmp/Case_1_index.delly2.db-info.tsv \ + --refseq-ser-path hg19_refseq.ser \ + --ensembl-ser-path hg19_ensembl.ser \ + --db-path /tmp/out.h2.db \ + --self-test-chr22-only + +awk -F $'\t' 'BEGIN { OFS=FS } { if (NR > 1) $17 = "UUID"; print $0; }' /tmp/Case_1_index.delly2.gts.tsv \ +> /tmp/Case_1_index.delly2.gts.tsv.replaced +diff /tmp/Case_1_index.delly2.gts.tsv.replaced Case_1_index.delly2.gts.tsv-expected +perl -p -i -e "s/${VERSION}/VERSION/g" /tmp/Case_1_index.delly2.db-info.tsv +diff /tmp/Case_1_index.delly2.db-info.tsv Case_1_index.delly2.db-info.tsv-expected +awk -F $'\t' 'BEGIN { OFS=FS } { if (NR > 1) $3 = "UUID"; print $0; }' /tmp/Case_1_index.delly2.feature-effects.tsv \ +> /tmp/Case_1_index.delly2.feature-effects.tsv.replaced +diff /tmp/Case_1_index.delly2.feature-effects.tsv.replaced Case_1_index.delly2.feature-effects.tsv-expected + +## if we reach here, everything is fine + +echo "-- ALL TESTS PASSED --" +exit 0 diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.db-info.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.db-info.tsv-expected deleted file mode 120000 index aaaebf4..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.db-info.tsv-expected +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.delly2.db-info.tsv-expected \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.db-info.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.db-info.tsv-expected new file mode 100644 index 0000000..79afba2 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.db-info.tsv-expected @@ -0,0 +1,9 @@ +genomebuild db_name release +GRCh37 clinvar for-testing +GRCh37 exac r1.0 +GRCh37 gnomad_exomes r2.1.1 +GRCh37 gnomad_genomes r2.1.1 +GRCh37 hgmd_public for-testing +GRCh37 thousand_genomes v3.20101123 +GRCh37 varfish-annotator VERSION +GRCh37 varfish-annotator-db for-testing diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.feature-effects.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.feature-effects.tsv-expected deleted file mode 120000 index c131795..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.feature-effects.tsv-expected +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.delly2.feature-effects.tsv-expected \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.feature-effects.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.feature-effects.tsv-expected new file mode 100644 index 0000000..595414c --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.feature-effects.tsv-expected @@ -0,0 +1,3 @@ +case_id set_id sv_uuid refseq_gene_id refseq_transcript_id refseq_transcript_coding refseq_effect ensembl_gene_id ensembl_transcript_id ensembl_transcript_coding ensembl_effect +. . UUID 51816 NM_017424.2 TRUE {"transcript_ablation","coding_transcript_variant"} ENSG00000093072 ENST00000262607.3 TRUE {"transcript_ablation","coding_transcript_variant"} +. . UUID 128954 NM_001037814.1 TRUE {"transcript_ablation","coding_transcript_variant"} ENSG00000215568 ENST00000400588.1 TRUE {"transcript_ablation","coding_transcript_variant"} diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.gts.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.gts.tsv-expected deleted file mode 120000 index c697b96..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.gts.tsv-expected +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.gts.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.gts.tsv-expected new file mode 100644 index 0000000..2625866 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.gts.tsv-expected @@ -0,0 +1,2 @@ +release chromosome chromosome_no bin chromosome2 chromosome_no2 bin2 pe_orientation start end start_ci_left start_ci_right end_ci_left end_ci_right case_id set_id sv_uuid caller sv_type sv_sub_type info num_hom_alt num_hom_ref num_het num_hemi_alt num_hemi_ref genotype +GRCh37 22 22 89 22 22 89 3to5 17400000 17700000 -29 29 -29 29 . . UUID EMBL.DELLYv1.1.3 DEL DEL {"""backgroundCarriers""":0,"""affectedCarriers""":0,"""unaffectedCarriers""":0} 0 2 1 0 0 {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ft""":{"""LowQual"""},"""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4,"""cn""":2},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":35,"""pec""":0,"""pev""":0,"""src""":29,"""srv""":2,"""cn""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":67,"""pec""":0,"""pev""":0,"""src""":32,"""srv""":1,"""cn""":2}} diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz deleted file mode 120000 index c4ce420..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.delly2.vcf.gz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz new file mode 100644 index 0000000..17af216 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz differ diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz.tbi deleted file mode 120000 index ce0ed93..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.delly2.vcf.gz.tbi \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz.tbi new file mode 100644 index 0000000..5af161a Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.delly2.vcf.gz.tbi differ diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.db-info.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.db-info.tsv-expected deleted file mode 120000 index 899cc75..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.db-info.tsv-expected +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.gatk_hc.db-info.tsv-expected \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.db-info.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.db-info.tsv-expected new file mode 100644 index 0000000..79afba2 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.db-info.tsv-expected @@ -0,0 +1,9 @@ +genomebuild db_name release +GRCh37 clinvar for-testing +GRCh37 exac r1.0 +GRCh37 gnomad_exomes r2.1.1 +GRCh37 gnomad_genomes r2.1.1 +GRCh37 hgmd_public for-testing +GRCh37 thousand_genomes v3.20101123 +GRCh37 varfish-annotator VERSION +GRCh37 varfish-annotator-db for-testing diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.gts.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.gts.tsv-expected deleted file mode 120000 index eae8039..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.gts.tsv-expected +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.gatk_hc.gts.tsv-expected \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.gts.tsv-expected b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.gts.tsv-expected new file mode 100644 index 0000000..98792b5 --- /dev/null +++ b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.gts.tsv-expected @@ -0,0 +1,167 @@ +release chromosome chromosome_no start end bin reference alternative var_type case_id set_id info genotype num_hom_alt num_hom_ref num_het num_hemi_alt num_hemi_ref in_clinvar exac_frequency exac_homozygous exac_heterozygous exac_hemizygous thousand_genomes_frequency thousand_genomes_homozygous thousand_genomes_heterozygous thousand_genomes_hemizygous gnomad_exomes_frequency gnomad_exomes_homozygous gnomad_exomes_heterozygous gnomad_exomes_hemizygous gnomad_genomes_frequency gnomad_genomes_homozygous gnomad_genomes_heterozygous gnomad_genomes_hemizygous refseq_gene_id refseq_transcript_id refseq_transcript_coding refseq_hgvs_c refseq_hgvs_p refseq_effect refseq_exon_dist ensembl_gene_id ensembl_transcript_id ensembl_transcript_coding ensembl_hgvs_c ensembl_hgvs_p ensembl_effect ensembl_exon_dist +GRCh37 22 22 17442987 17442987 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":52,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.199719 118 759 0 0 0 0 0 0.164199 494 4157 0 128954 NM_001037814.1 TRUE c.*636G>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.*636G>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17443131 17443131 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":54,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":52,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.199117 118 756 0 0 0 0 0 0.164276 497 4160 0 128954 NM_001037814.1 TRUE c.*492A>G p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.*492A>G p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17443238 17443238 718 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":48,"""gq""":99}} 0 0 3 0 0 FALSE 0 0 0 0 0.547973 750 1230 0 0 0 0 0 0.574144 5255 7494 0 128954 NM_001037814.1 TRUE c.*385A>T p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.*385A>T p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17444231 17444231 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":45,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0614211 21 264 0 0 0 0 0 0.0819131 137 2283 0 128954 NM_001037814.1 TRUE c.1581+384A>G p.= {"coding_transcript_intron_variant"} 384 ENSG00000215568 ENST00000400588.1 TRUE c.1581+384A>G p.= {"coding_transcript_intron_variant"} 384 +GRCh37 22 22 17445502 17445502 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":46,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":37,"""gq""":99}} 0 0 3 0 0 FALSE 0 0 0 0 0.546166 745 1231 0 0 0 0 0 0.56894 5120 7561 0 128954 NM_001037814.1 TRUE c.1476+154T>G p.= {"coding_transcript_intron_variant"} 154 ENSG00000215568 ENST00000400588.1 TRUE c.1476+154T>G p.= {"coding_transcript_intron_variant"} 154 +GRCh37 22 22 17446715 17446715 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":32,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":30,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0863107 30 370 0 0 0 0 0 0.102647 169 2881 0 128954 NM_001037814.1 TRUE c.1288+275C>T p.= {"coding_transcript_intron_variant"} 275 ENSG00000215568 ENST00000400588.1 TRUE c.1288+275C>T p.= {"coding_transcript_intron_variant"} 275 +GRCh37 22 22 17446906 17446906 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0863107 29 372 0 0 0 0 0 0.102198 167 2874 0 128954 NM_001037814.1 TRUE c.1288+84C>T p.= {"coding_transcript_intron_variant"} 84 ENSG00000215568 ENST00000400588.1 TRUE c.1288+84C>T p.= {"coding_transcript_intron_variant"} 84 +GRCh37 22 22 17446914 17446914 718 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.203934 127 762 0 0 0 0 0 0.172011 549 4298 0 128954 NM_001037814.1 TRUE c.1288+76A>C p.= {"coding_transcript_intron_variant"} 76 ENSG00000215568 ENST00000400588.1 TRUE c.1288+76A>C p.= {"coding_transcript_intron_variant"} 76 +GRCh37 22 22 17446991 17446991 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96}} 2 0 1 0 0 FALSE 0.772 36326 20475 0 0.825171 1718 675 0 0.777145 76015 41605 0 0.808722 10388 4592 0 128954 NM_001037814.1 TRUE c.1287G>A p.= {"splice_region_variant","synonymous_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.1287G>A p.= {"splice_region_variant","synonymous_variant"} 0 +GRCh37 22 22 17447350 17447350 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":21,"""gq""":63},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":43,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.00521879 1 24 0 0 0 0 0 0.00850698 1 265 0 128954 NM_001037814.1 TRUE c.1024-96C>T p.= {"coding_transcript_intron_variant"} 96 ENSG00000215568 ENST00000400588.1 TRUE c.1024-96C>T p.= {"coding_transcript_intron_variant"} 96 +GRCh37 22 22 17447438 17447438 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.742272 1375 948 0 0 0 0 0 0.738208 8572 5987 0 128954 NM_001037814.1 TRUE c.1024-184C>T p.= {"coding_transcript_intron_variant"} 184 ENSG00000215568 ENST00000400588.1 TRUE c.1024-184C>T p.= {"coding_transcript_intron_variant"} 184 +GRCh37 22 22 17448143 17448143 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":51,"""dp""":51,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.823766 1717 670 0 0 0 0 0 0.807349 10267 4602 0 128954 NM_001037814.1 TRUE c.1024-889C>T p.= {"coding_transcript_intron_variant"} 889 ENSG00000215568 ENST00000400588.1 TRUE c.1024-889C>T p.= {"coding_transcript_intron_variant"} 889 +GRCh37 22 22 17449076 17449076 718 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":50,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":25,"""gq""":75},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":50,"""dp""":50,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.826576 1721 676 0 0 0 0 0 0.809263 10396 4580 0 128954 NM_001037814.1 TRUE c.1023+112G>C p.= {"coding_transcript_intron_variant"} 112 ENSG00000215568 ENST00000400588.1 TRUE c.1023+112G>C p.= {"coding_transcript_intron_variant"} 112 +GRCh37 22 22 17451528 17451528 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":29,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":16,"""gq""":48},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":36,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0301084 3 144 0 0 0 0 0 0.0404552 40 1189 0 128954 NM_001037814.1 TRUE c.687-445C>T p.= {"coding_transcript_intron_variant"} 445 ENSG00000215568 ENST00000400588.1 TRUE c.687-445C>T p.= {"coding_transcript_intron_variant"} 445 +GRCh37 22 22 17451613 17451613 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":25,"""gq""":75},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":35,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0576074 9 269 0 0 0 0 0 0.0939713 135 2676 0 128954 NM_001037814.1 TRUE c.687-530G>A p.= {"coding_transcript_intron_variant"} 530 ENSG00000215568 ENST00000400588.1 TRUE c.687-530G>A p.= {"coding_transcript_intron_variant"} 530 +GRCh37 22 22 17451710 17451710 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":42,"""gq""":99}} 0 0 3 0 0 FALSE 0 0 0 0 0.135688 59 558 0 0 0 0 0 0.191286 604 4785 0 128954 NM_001037814.1 TRUE c.687-627A>G p.= {"coding_transcript_intron_variant"} 627 ENSG00000215568 ENST00000400588.1 TRUE c.687-627A>G p.= {"coding_transcript_intron_variant"} 627 +GRCh37 22 22 17451854 17451854 718 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.155761 120 536 0 0 0 0 0 0.161126 550 3931 0 128954 NM_001037814.1 TRUE c.687-771C>G p.= {"coding_transcript_intron_variant"} 771 ENSG00000215568 ENST00000400588.1 TRUE c.687-771C>G p.= {"coding_transcript_intron_variant"} 771 +GRCh37 22 22 17451883 17451883 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":34,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0600161 9 281 0 0 0 0 0 0.0942456 135 2642 0 128954 NM_001037814.1 TRUE c.687-800G>T p.= {"coding_transcript_intron_variant"} 800 ENSG00000215568 ENST00000400588.1 TRUE c.687-800G>T p.= {"coding_transcript_intron_variant"} 800 +GRCh37 22 22 17452300 17452300 718 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":26,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":1,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0666399 21 290 0 0 0 0 0 0.0901733 160 2510 0 128954 NM_001037814.1 TRUE c.687-1217A>C p.= {"coding_transcript_intron_variant"} 1217 ENSG00000215568 ENST00000400588.1 TRUE c.687-1217A>C p.= {"coding_transcript_intron_variant"} 1217 +GRCh37 22 22 17452925 17452925 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":54,"""dp""":54,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.816339 1681 705 0 0 0 0 0 0.792801 10023 4821 0 128954 NM_001037814.1 TRUE c.687-1842C>T p.= {"coding_transcript_intron_variant"} 1842 ENSG00000215568 ENST00000400588.1 TRUE c.687-1842C>T p.= {"coding_transcript_intron_variant"} 1842 +GRCh37 22 22 17452966 17452966 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.848254 1814 598 0 0 0 0 0 0.834035 11024 4119 0 128954 NM_001037814.1 TRUE c.687-1883A>G p.= {"coding_transcript_intron_variant"} 1883 ENSG00000215568 ENST00000400588.1 TRUE c.687-1883A>G p.= {"coding_transcript_intron_variant"} 1883 +GRCh37 22 22 17453588 17453588 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.685468 1177 1061 0 0 0 0 0 0.672935 7102 6836 0 128954 NM_001037814.1 TRUE c.687-2505T>G p.= {"coding_transcript_intron_variant"} 2505 ENSG00000215568 ENST00000400588.1 TRUE c.687-2505T>G p.= {"coding_transcript_intron_variant"} 2505 +GRCh37 22 22 17453844 17453844 718 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":24,"""gq""":72},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.205339 132 759 0 0 0 0 0 0.164773 524 4114 0 128954 NM_001037814.1 TRUE c.687-2761T>A p.= {"coding_transcript_intron_variant"} 2761 ENSG00000215568 ENST00000400588.1 TRUE c.687-2761T>A p.= {"coding_transcript_intron_variant"} 2761 +GRCh37 22 22 17453902 17453902 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":44,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0612204 11 283 0 0 0 0 0 0.0930292 133 2654 0 128954 NM_001037814.1 TRUE c.687-2819C>T p.= {"coding_transcript_intron_variant"} 2819 ENSG00000215568 ENST00000400588.1 TRUE c.687-2819C>T p.= {"coding_transcript_intron_variant"} 2819 +GRCh37 22 22 17454486 17454486 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":20,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":51,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.229627 171 802 0 0 0 0 0 0.184175 671 4433 0 128954 NM_001037814.1 TRUE c.687-3403A>G p.= {"coding_transcript_intron_variant"} 3403 ENSG00000215568 ENST00000400588.1 TRUE c.687-3403A>G p.= {"coding_transcript_intron_variant"} 3403 +GRCh37 22 22 17454695 17454695 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":24,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":34,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.204737 132 756 0 0 0 0 0 0.164029 516 4108 0 128954 NM_001037814.1 TRUE c.687-3612G>A p.= {"coding_transcript_intron_variant"} 3612 ENSG00000215568 ENST00000400588.1 TRUE c.687-3612G>A p.= {"coding_transcript_intron_variant"} 3612 +GRCh37 22 22 17454945 17454945 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":27,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.20554 134 756 0 0 0 0 0 0.164201 518 4114 0 128954 NM_001037814.1 TRUE c.687-3862C>T p.= {"coding_transcript_intron_variant"} 3862 ENSG00000215568 ENST00000400588.1 TRUE c.687-3862C>T p.= {"coding_transcript_intron_variant"} 3862 +GRCh37 22 22 17455630 17455630 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.823766 1712 680 0 0 0 0 0 0.804978 10302 4624 0 128954 NM_001037814.1 TRUE c.687-4547G>T p.= {"coding_transcript_intron_variant"} 4547 ENSG00000215568 ENST00000400588.1 TRUE c.687-4547G>T p.= {"coding_transcript_intron_variant"} 4547 +GRCh37 22 22 17455735 17455735 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.205339 132 759 0 0 0 0 0 0.164699 522 4117 0 128954 NM_001037814.1 TRUE c.687-4652C>T p.= {"coding_transcript_intron_variant"} 4652 ENSG00000215568 ENST00000400588.1 TRUE c.687-4652C>T p.= {"coding_transcript_intron_variant"} 4652 +GRCh37 22 22 17456370 17456370 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825773 1719 676 0 0 0 0 0 0.804933 10307 4611 0 128954 NM_001037814.1 TRUE c.687-5287T>C p.= {"coding_transcript_intron_variant"} 5287 ENSG00000215568 ENST00000400588.1 TRUE c.687-5287T>C p.= {"coding_transcript_intron_variant"} 5287 +GRCh37 22 22 17456642 17456642 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":44,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.79988 1623 739 0 0 0 0 0 0.78203 9715 5010 0 128954 NM_001037814.1 TRUE c.687-5559G>T p.= {"coding_transcript_intron_variant"} 5559 ENSG00000215568 ENST00000400588.1 TRUE c.687-5559G>T p.= {"coding_transcript_intron_variant"} 5559 +GRCh37 22 22 17456879 17456879 718 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":28,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":44,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0977519 38 411 0 0 0 0 0 0.117852 203 3110 0 128954 NM_001037814.1 TRUE c.687-5797_687-5796insT p.= {"coding_transcript_intron_variant"} 5796 ENSG00000215568 ENST00000400588.1 TRUE c.687-5797_687-5796insT p.= {"coding_transcript_intron_variant"} 5796 +GRCh37 22 22 17457136 17457136 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825773 1719 676 0 0 0 0 0 0.805407 10312 4611 0 128954 NM_001037814.1 TRUE c.687-6053A>G p.= {"coding_transcript_intron_variant"} 6053 ENSG00000215568 ENST00000400588.1 TRUE c.687-6053A>G p.= {"coding_transcript_intron_variant"} 6053 +GRCh37 22 22 17457276 17457276 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825974 1720 675 0 0 0 0 0 0.80503 10320 4617 0 128954 NM_001037814.1 TRUE c.687-6193G>A p.= {"coding_transcript_intron_variant"} 6193 ENSG00000215568 ENST00000400588.1 TRUE c.687-6193G>A p.= {"coding_transcript_intron_variant"} 6193 +GRCh37 22 22 17457761 17457761 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0640305 12 295 0 0 0 0 0 0.0946325 141 2687 0 128954 NM_001037814.1 TRUE c.687-6678A>G p.= {"coding_transcript_intron_variant"} 6678 ENSG00000215568 ENST00000400588.1 TRUE c.687-6678A>G p.= {"coding_transcript_intron_variant"} 6678 +GRCh37 22 22 17457979 17457979 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":90},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.826174 1720 676 0 0 0 0 0 0.805329 10318 4603 0 128954 NM_001037814.1 TRUE c.687-6896T>C p.= {"coding_transcript_intron_variant"} 6896 ENSG00000215568 ENST00000400588.1 TRUE c.687-6896T>C p.= {"coding_transcript_intron_variant"} 6896 +GRCh37 22 22 17458083 17458083 718 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":93},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":28,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0634283 12 292 0 0 0 0 0 0.0941345 138 2677 0 128954 NM_001037814.1 TRUE c.687-7000C>A p.= {"coding_transcript_intron_variant"} 7000 ENSG00000215568 ENST00000400588.1 TRUE c.687-7000C>A p.= {"coding_transcript_intron_variant"} 7000 +GRCh37 22 22 17458238 17458238 718 C CAA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":9,"""dp""":19,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":32,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.140305 26 647 0 0 0 0 0 0.222272 375 3186 0 128954 NM_001037814.1 TRUE c.687-7156_687-7155insTT p.= {"coding_transcript_intron_variant"} 7155 ENSG00000215568 ENST00000400588.1 TRUE c.687-7156_687-7155insTT p.= {"coding_transcript_intron_variant"} 7155 +GRCh37 22 22 17458882 17458882 718 A AGACAC indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.491369 594 1260 0 0 0 0 0 0.485924 3708 7739 0 128954 NM_001037814.1 TRUE c.687-7800_687-7799insGTGTC p.= {"coding_transcript_intron_variant"} 7799 ENSG00000215568 ENST00000400588.1 TRUE c.687-7800_687-7799insGTGTC p.= {"coding_transcript_intron_variant"} 7799 +GRCh37 22 22 17458962 17458963 718 GA G indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.800482 1623 742 0 0 0 0 0 0.781987 9732 5020 0 128954 NM_001037814.1 TRUE c.687-7880del p.= {"coding_transcript_intron_variant"} 7879 ENSG00000215568 ENST00000400588.1 TRUE c.687-7880del p.= {"coding_transcript_intron_variant"} 7879 +GRCh37 22 22 17459768 17459768 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":28,"""gq""":84}} 0 1 2 0 0 FALSE 0 0 0 0 0.0600161 20 259 0 0 0 0 0 0.0872682 162 2415 0 128954 NM_001037814.1 TRUE c.687-8685A>G p.= {"coding_transcript_intron_variant"} 8685 ENSG00000215568 ENST00000400588.1 TRUE c.687-8685A>G p.= {"coding_transcript_intron_variant"} 8685 +GRCh37 22 22 17460357 17460357 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 0.999873 15689 4 0 128954 NM_001037814.1 TRUE c.686+8493T>C p.= {"coding_transcript_intron_variant"} 8493 ENSG00000215568 ENST00000400588.1 TRUE c.686+8493T>C p.= {"coding_transcript_intron_variant"} 8493 +GRCh37 22 22 17461883 17461883 718 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":21,"""gq""":61}} 0 1 2 0 0 FALSE 0 0 0 0 0.03332 9 148 0 0 0 0 0 0.0641271 92 1826 0 128954 NM_001037814.1 TRUE c.686+6967T>A p.= {"coding_transcript_intron_variant"} 6967 ENSG00000215568 ENST00000400588.1 TRUE c.686+6967T>A p.= {"coding_transcript_intron_variant"} 6967 +GRCh37 22 22 17462185 17462185 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":28,"""dp""":28,"""gq""":84},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.812124 1673 700 0 0 0 0 0 0.768057 9213 4989 0 128954 NM_001037814.1 TRUE c.686+6665G>T p.= {"coding_transcript_intron_variant"} 6665 ENSG00000215568 ENST00000400588.1 TRUE c.686+6665G>T p.= {"coding_transcript_intron_variant"} 6665 +GRCh37 22 22 17463189 17463189 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":25,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":57,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0953432 41 393 0 0 0 0 0 0.115546 224 3176 0 128954 NM_001037814.1 TRUE c.686+5661A>G p.= {"coding_transcript_intron_variant"} 5661 ENSG00000215568 ENST00000400588.1 TRUE c.686+5661A>G p.= {"coding_transcript_intron_variant"} 5661 +GRCh37 22 22 17463620 17463620 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":54,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":2,"""dp""":33,"""gq""":78}} 0 1 2 0 0 FALSE 0 0 0 0 0.0951425 40 394 0 0 0 0 0 0.115497 223 3179 0 128954 NM_001037814.1 TRUE c.686+5230T>G p.= {"coding_transcript_intron_variant"} 5230 ENSG00000215568 ENST00000400588.1 TRUE c.686+5230T>G p.= {"coding_transcript_intron_variant"} 5230 +GRCh37 22 22 17467411 17467411 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":39,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0648334 11 301 0 0 0 0 0 0.0956796 146 2711 0 128954 NM_001037814.1 TRUE c.686+1439C>T p.= {"coding_transcript_intron_variant"} 1439 ENSG00000215568 ENST00000400588.1 TRUE c.686+1439C>T p.= {"coding_transcript_intron_variant"} 1439 +GRCh37 22 22 17467474 17467474 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":28,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.823966 1711 683 0 0 0 0 0 0.805167 10309 4624 0 128954 NM_001037814.1 TRUE c.686+1376G>T p.= {"coding_transcript_intron_variant"} 1376 ENSG00000215568 ENST00000400588.1 TRUE c.686+1376G>T p.= {"coding_transcript_intron_variant"} 1376 +GRCh37 22 22 17467684 17467684 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":35,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0642312 11 298 0 0 0 0 0 0.0956491 144 2715 0 128954 NM_001037814.1 TRUE c.686+1166C>T p.= {"coding_transcript_intron_variant"} 1166 ENSG00000215568 ENST00000400588.1 TRUE c.686+1166C>T p.= {"coding_transcript_intron_variant"} 1166 +GRCh37 22 22 17469664 17469664 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":42,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0638298 11 296 0 0 0 0 0 0.0954415 144 2706 0 128954 NM_001037814.1 TRUE c.479-607C>T p.= {"coding_transcript_intron_variant"} 607 ENSG00000215568 ENST00000400588.1 TRUE c.479-607C>T p.= {"coding_transcript_intron_variant"} 607 +GRCh37 22 22 17470779 17470779 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":45,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.160779 89 623 0 0 0 0 0 0.134506 362 3496 0 128954 NM_001037814.1 TRUE c.479-1722G>T p.= {"coding_transcript_intron_variant"} 1722 ENSG00000215568 ENST00000400588.1 TRUE c.479-1722G>T p.= {"coding_transcript_intron_variant"} 1722 +GRCh37 22 22 17471354 17471354 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.20012 125 747 0 0 0 0 0 0.161509 504 4054 0 128954 NM_001037814.1 TRUE c.478+1409G>A p.= {"coding_transcript_intron_variant"} 1409 ENSG00000215568 ENST00000400588.1 TRUE c.478+1409G>A p.= {"coding_transcript_intron_variant"} 1409 +GRCh37 22 22 17471886 17471887 718 AT A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0164593 0 82 0 0 0 0 0 0.0236654 16 711 0 128954 NM_001037814.1 TRUE c.478+876del p.= {"coding_transcript_intron_variant"} 876 ENSG00000215568 ENST00000400588.1 TRUE c.478+876del p.= {"coding_transcript_intron_variant"} 876 +GRCh37 22 22 17472071 17472071 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":25,"""gq""":75},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825974 1719 677 0 0 0 0 0 0.805879 10261 4565 0 128954 NM_001037814.1 TRUE c.478+692T>C p.= {"coding_transcript_intron_variant"} 692 ENSG00000215568 ENST00000400588.1 TRUE c.478+692T>C p.= {"coding_transcript_intron_variant"} 692 +GRCh37 22 22 17472134 17472134 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":92},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":34,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.00722601 2 32 0 0 0 0 0 0.0160254 6 487 0 128954 NM_001037814.1 TRUE c.478+629A>G p.= {"coding_transcript_intron_variant"} 629 ENSG00000215568 ENST00000400588.1 TRUE c.478+629A>G p.= {"coding_transcript_intron_variant"} 629 +GRCh37 22 22 17473888 17473888 718 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0949418 39 395 0 0 0 0 0 0.115083 221 3167 0 128954 NM_001037814.1 TRUE c.175-822C>G p.= {"coding_transcript_intron_variant"} 822 ENSG00000215568 ENST00000400588.1 TRUE c.175-822C>G p.= {"coding_transcript_intron_variant"} 822 +GRCh37 22 22 17474812 17474812 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96}} 2 0 1 0 0 FALSE 0 0 0 0 0.828382 1727 673 0 0 0 0 0 0.805875 10319 4602 0 128954 NM_001037814.1 TRUE c.175-1746T>C p.= {"coding_transcript_intron_variant"} 1746 ENSG00000215568 ENST00000400588.1 TRUE c.175-1746T>C p.= {"coding_transcript_intron_variant"} 1746 +GRCh37 22 22 17475921 17475921 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":58,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":50,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":37,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.180851 112 677 0 0 0 0 0 0.145361 413 3736 0 128954 NM_001037814.1 TRUE c.175-2855A>G p.= {"coding_transcript_intron_variant"} 2855 ENSG00000215568 ENST00000400588.1 TRUE c.175-2855A>G p.= {"coding_transcript_intron_variant"} 2855 +GRCh37 22 22 17476064 17476064 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":24,"""gq""":72},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":25,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0662385 13 304 0 0 0 0 0 0.097379 147 2760 0 128954 NM_001037814.1 TRUE c.175-2998A>G p.= {"coding_transcript_intron_variant"} 2998 ENSG00000215568 ENST00000400588.1 TRUE c.175-2998A>G p.= {"coding_transcript_intron_variant"} 2998 +GRCh37 22 22 17476702 17476702 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":31,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0660377 13 303 0 0 0 0 0 0.0973993 149 2758 0 128954 NM_001037814.1 TRUE c.175-3636T>G p.= {"coding_transcript_intron_variant"} 3636 ENSG00000215568 ENST00000400588.1 TRUE c.175-3636T>G p.= {"coding_transcript_intron_variant"} 3636 +GRCh37 22 22 17477589 17477589 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":28,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":17,"""dp""":17,"""gq""":51},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":29,"""dp""":44,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.334404 325 1016 0 0 0 0 0 0.307032 1598 6419 0 128954 NM_001037814.1 TRUE c.175-4523T>C p.= {"coding_transcript_intron_variant"} 4523 ENSG00000215568 ENST00000400588.1 TRUE c.175-4523T>C p.= {"coding_transcript_intron_variant"} 4523 +GRCh37 22 22 17477688 17477688 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":16,"""dp""":16,"""gq""":48},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":7,"""dp""":7,"""gq""":24},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":7,"""dp""":7,"""gq""":21}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 1.0 15381 0 0 128954 NM_001037814.1 TRUE c.175-4622T>G p.= {"coding_transcript_intron_variant"} 4622 ENSG00000215568 ENST00000400588.1 TRUE c.175-4622T>G p.= {"coding_transcript_intron_variant"} 4622 +GRCh37 22 22 17477706 17477706 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":5,"""dp""":15,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":10,"""dp""":10,"""gq""":30},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":8,"""dp""":8,"""gq""":24}} 2 0 1 0 0 FALSE 0 0 0 0 0.826174 1719 678 0 0 0 0 0 0.795531 7640 3730 0 128954 NM_001037814.1 TRUE c.175-4640A>G p.= {"coding_transcript_intron_variant"} 4640 ENSG00000215568 ENST00000400588.1 TRUE c.175-4640A>G p.= {"coding_transcript_intron_variant"} 4640 +GRCh37 22 22 17477859 17477859 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":20,"""gq""":60},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":22,"""gq""":66}} 0 2 1 0 0 FALSE 0 0 0 0 0.0250903 4 117 0 0 0 0 0 0.0364175 38 1067 0 128954 NM_001037814.1 TRUE c.175-4793A>G p.= {"coding_transcript_intron_variant"} 4793 ENSG00000215568 ENST00000400588.1 TRUE c.175-4793A>G p.= {"coding_transcript_intron_variant"} 4793 +GRCh37 22 22 17478236 17478236 718 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":46,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0018065 0 9 0 0 0 0 0 0.00764283 0 240 0 128954 NM_001037814.1 TRUE c.175-5170A>T p.= {"coding_transcript_intron_variant"} 5170 ENSG00000215568 ENST00000400588.1 TRUE c.175-5170A>T p.= {"coding_transcript_intron_variant"} 5170 +GRCh37 22 22 17478728 17478728 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":49,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0592132 20 255 0 0 0 0 0 0.0866046 162 2394 0 128954 NM_001037814.1 TRUE c.175-5662C>T p.= {"coding_transcript_intron_variant"} 5662 ENSG00000215568 ENST00000400588.1 TRUE c.175-5662C>T p.= {"coding_transcript_intron_variant"} 5662 +GRCh37 22 22 17479400 17479400 718 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":1,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":51,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.200723 126 748 0 0 0 0 0 0.161319 504 4050 0 128954 NM_001037814.1 TRUE c.175-6334C>A p.= {"coding_transcript_intron_variant"} 6334 ENSG00000215568 ENST00000400588.1 TRUE c.175-6334C>A p.= {"coding_transcript_intron_variant"} 6334 +GRCh37 22 22 17480064 17480064 718 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":28,"""gq""":84},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":37,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0656363 13 301 0 0 0 0 0 0.0961771 143 2733 0 128954 NM_001037814.1 TRUE c.175-6998A>T p.= {"coding_transcript_intron_variant"} 6998 ENSG00000215568 ENST00000400588.1 TRUE c.175-6998A>T p.= {"coding_transcript_intron_variant"} 6998 +GRCh37 22 22 17481048 17481048 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.824769 1711 687 0 0 0 0 0 0.804312 10289 4642 0 128954 NM_001037814.1 TRUE c.174+7783A>G p.= {"coding_transcript_intron_variant"} 7783 ENSG00000215568 ENST00000400588.1 TRUE c.174+7783A>G p.= {"coding_transcript_intron_variant"} 7783 +GRCh37 22 22 17481355 17481355 718 C CT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":10,"""dp""":24,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0650341 21 282 0 0 0 0 0 0.0867961 141 2400 0 128954 NM_001037814.1 TRUE c.174+7475_174+7476insA p.= {"coding_transcript_intron_variant"} 7476 ENSG00000215568 ENST00000400588.1 TRUE c.174+7475_174+7476insA p.= {"coding_transcript_intron_variant"} 7476 +GRCh37 22 22 17482086 17482086 718 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":42,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0620233 11 287 0 0 0 0 0 0.0942121 140 2676 0 128954 NM_001037814.1 TRUE c.174+6745C>A p.= {"coding_transcript_intron_variant"} 6745 ENSG00000215568 ENST00000400588.1 TRUE c.174+6745C>A p.= {"coding_transcript_intron_variant"} 6745 +GRCh37 22 22 17482227 17482227 718 T TC indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":25,"""gq""":75}} 0 2 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 3.18492E-5 0 1 0 128954 NM_001037814.1 TRUE c.174+6603_174+6604insG p.= {"coding_transcript_intron_variant"} 6604 ENSG00000215568 ENST00000400588.1 TRUE c.174+6603_174+6604insG p.= {"coding_transcript_intron_variant"} 6604 +GRCh37 22 22 17482825 17482825 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825773 1719 676 0 0 0 0 0 0.806073 10334 4604 0 128954 NM_001037814.1 TRUE c.174+6006T>C p.= {"coding_transcript_intron_variant"} 6006 ENSG00000215568 ENST00000400588.1 TRUE c.174+6006T>C p.= {"coding_transcript_intron_variant"} 6006 +GRCh37 22 22 17482847 17482847 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":48,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.160177 88 622 0 0 0 0 0 0.134098 356 3496 0 128954 NM_001037814.1 TRUE c.174+5984G>A p.= {"coding_transcript_intron_variant"} 5984 ENSG00000215568 ENST00000400588.1 TRUE c.174+5984G>A p.= {"coding_transcript_intron_variant"} 5984 +GRCh37 22 22 17483804 17483805 718 AG A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":34,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0636291 12 293 0 0 0 0 0 0.0944232 138 2687 0 128954 NM_001037814.1 TRUE c.174+5026del p.= {"coding_transcript_intron_variant"} 5026 ENSG00000215568 ENST00000400588.1 TRUE c.174+5026del p.= {"coding_transcript_intron_variant"} 5026 +GRCh37 22 22 17484650 17484650 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":34,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0664392 15 301 0 0 0 0 0 0.0973152 143 2766 0 128954 NM_001037814.1 TRUE c.174+4181T>G p.= {"coding_transcript_intron_variant"} 4181 ENSG00000215568 ENST00000400588.1 TRUE c.174+4181T>G p.= {"coding_transcript_intron_variant"} 4181 +GRCh37 22 22 17484733 17484733 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0116419 2 54 0 0 0 0 0 0.0227854 13 687 0 128954 NM_001037814.1 TRUE c.174+4098A>G p.= {"coding_transcript_intron_variant"} 4098 ENSG00000215568 ENST00000400588.1 TRUE c.174+4098A>G p.= {"coding_transcript_intron_variant"} 4098 +GRCh37 22 22 17486937 17486937 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":36,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.068045 15 309 0 0 0 0 0 0.0973612 145 2765 0 128954 NM_001037814.1 TRUE c.174+1894A>G p.= {"coding_transcript_intron_variant"} 1894 ENSG00000215568 ENST00000400588.1 TRUE c.174+1894A>G p.= {"coding_transcript_intron_variant"} 1894 +GRCh37 22 22 17488430 17488430 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":31,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":89}} 0 1 2 0 0 FALSE 0 0 0 0 0.0796869 27 343 0 0 0 0 0 0.102473 176 2731 0 128954 NM_001037814.1 TRUE c.174+401A>G p.= {"coding_transcript_intron_variant"} 401 ENSG00000215568 ENST00000400588.1 TRUE c.174+401A>G p.= {"coding_transcript_intron_variant"} 401 +GRCh37 22 22 17488669 17488669 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.809314 1639 754 0 0 0 0 0 0.794817 9984 4905 0 128954 NM_001037814.1 TRUE c.174+162G>A p.= {"coding_transcript_intron_variant"} 162 ENSG00000215568 ENST00000400588.1 TRUE c.174+162G>A p.= {"coding_transcript_intron_variant"} 162 +GRCh37 22 22 17488727 17488727 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":50,"""dp""":50,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.813328 1653 746 0 0 0 0 0 0.796328 10009 4880 0 128954 NM_001037814.1 TRUE c.174+104T>G p.= {"coding_transcript_intron_variant"} 104 ENSG00000215568 ENST00000400588.1 TRUE c.174+104T>G p.= {"coding_transcript_intron_variant"} 104 +GRCh37 22 22 17488823 17488823 718 C CG indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 2 0 1 0 0 FALSE 0.783 32903 17465 0 0.8334 1750 652 0 0.794509 72468 35945 0 0.832189 10914 4108 0 128954 NM_001037814.1 TRUE c.174+7_174+8insC p.? {"splice_region_variant","coding_transcript_intron_variant"} 8 ENSG00000215568 ENST00000400588.1 TRUE c.174+7_174+8insC p.? {"splice_region_variant","coding_transcript_intron_variant"} 8 +GRCh37 22 22 17660303 17660303 719 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":26,"""gq""":78},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":36,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.293456 209 1044 0 0 0 0 0 0.350284 1934 7112 0 51816 NM_017424.2 TRUE c.*2070T>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*2070T>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17660501 17660501 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":36,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.581092 930 1035 0 0 0 0 0 0.626397 6408 6804 0 51816 NM_017424.2 TRUE c.*1872G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1872G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17660556 17660556 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":26,"""gq""":78},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.234243 174 819 0 0 0 0 0 0.294155 1465 6260 0 51816 NM_017424.2 TRUE c.*1817A>G p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1817A>G p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17660646 17660646 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":42,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.282417 205 997 0 0 0 0 0 0.30896 1520 6636 0 51816 NM_017424.2 TRUE c.*1727T>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1727T>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661178 17661178 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.335006 311 1047 0 0 0 0 0 0.36062 2174 6943 0 51816 NM_017424.2 TRUE c.*1195T>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1195T>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661347 17661347 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":27,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":22,"""gq""":66},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":30,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.173023 93 676 0 0 0 0 0 0.241923 974 5630 0 51816 NM_017424.2 TRUE c.*1026G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1026G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661764 17661764 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":34,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.228824 152 836 0 0 0 0 0 0.314218 1612 6628 0 51816 NM_017424.2 TRUE c.*609A>G p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*609A>G p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661791 17661791 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":32,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.172822 93 675 0 0 0 0 0 0.241588 975 5618 0 51816 NM_017424.2 TRUE c.*582G>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*582G>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661922 17661922 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.290044 265 915 0 0 0 0 0 0.364383 2175 7053 0 51816 NM_017424.2 TRUE c.*451G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*451G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661935 17661935 719 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":43,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.170213 92 664 0 0 0 0 0 0.239793 959 5600 0 51816 NM_017424.2 TRUE c.*438T>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*438T>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17662163 17662163 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":50,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.564231 851 1109 0 0 0 0 0 0.606041 5919 7142 0 51816 NM_017424.2 TRUE c.*210G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*210G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17662591 17662591 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":40,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":53,"""gq""":99}} 1 0 2 0 0 TRUE 0 0 0 0 0.186672 116 698 0 0 0 0 0 0.275653 1281 6072 0 51816 NM_017424.2 TRUE c.1442+119G>C p.= {"coding_transcript_intron_variant"} 119 ENSG00000093072 ENST00000262607.3 TRUE c.1442+119G>C p.= {"coding_transcript_intron_variant"} 119 +GRCh37 22 22 17662679 17662679 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":44,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":53,"""gq""":99}} 1 0 2 0 0 TRUE 0.249 4266 21428 0 0.187073 116 700 0 0.246776 8757 43681 0 0.276069 1292 6068 0 51816 NM_017424.2 TRUE c.1442+31G>A p.= {"coding_transcript_intron_variant"} 31 ENSG00000093072 ENST00000262607.3 TRUE c.1442+31G>A p.= {"coding_transcript_intron_variant"} 31 +GRCh37 22 22 17662699 17662699 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":54,"""gq""":99}} 1 0 2 0 0 TRUE 0.256 4594 21824 0 0.187073 112 708 0 0.255625 9560 44934 0 0.281751 1332 6161 0 51816 NM_017424.2 TRUE c.1442+11T>C p.= {"coding_transcript_intron_variant"} 11 ENSG00000093072 ENST00000262607.3 TRUE c.1442+11T>C p.= {"coding_transcript_intron_variant"} 11 +GRCh37 22 22 17662793 17662793 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":42,"""gq""":99}} 1 0 2 0 0 TRUE 0.256 4612 21901 0 0.19169 116 723 0 0.255784 9566 45173 0 0.285112 1360 6212 0 51816 NM_017424.2 TRUE c.1359T>C p.= {"synonymous_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.1359T>C p.= {"synonymous_variant"} 0 +GRCh37 22 22 17662917 17662917 719 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":30,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 1 0 2 0 0 TRUE 0.248 4256 21433 0 0.18607 113 701 0 0.246352 8773 43839 0 0.274796 1272 6056 0 51816 NM_017424.2 TRUE c.1240-5C>G p.? {"splice_region_variant","coding_transcript_intron_variant"} 5 ENSG00000093072 ENST00000262607.3 TRUE c.1240-5C>G p.? {"splice_region_variant","coding_transcript_intron_variant"} 5 +GRCh37 22 22 17663117 17663117 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":30,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":37,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.192694 116 728 0 0 0 0 0 0.283339 1327 6206 0 51816 NM_017424.2 TRUE c.1240-205A>G p.= {"coding_transcript_intron_variant"} 205 ENSG00000093072 ENST00000262607.3 TRUE c.1240-205A>G p.= {"coding_transcript_intron_variant"} 205 +GRCh37 22 22 17663127 17663127 719 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.475713 674 1022 0 0 0 0 0 0.553134 5025 7231 0 51816 NM_017424.2 TRUE c.1240-215C>A p.= {"coding_transcript_intron_variant"} 215 ENSG00000093072 ENST00000262607.3 TRUE c.1240-215C>A p.= {"coding_transcript_intron_variant"} 215 +GRCh37 22 22 17664296 17664296 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":31,"""dp""":31,"""gq""":93},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":26,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.194701 119 732 0 0 0 0 0 0.286257 1320 6179 0 51816 NM_017424.2 TRUE c.1082-645G>C p.= {"coding_transcript_intron_variant"} 645 ENSG00000093072 ENST00000262607.3 TRUE c.1082-645G>C p.= {"coding_transcript_intron_variant"} 645 +GRCh37 22 22 17664307 17664307 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":26,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":10,"""dp""":23,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.191088 118 716 0 0 0 0 0 0.278172 1254 6043 0 51816 NM_017424.2 TRUE c.1082-656G>A p.= {"coding_transcript_intron_variant"} 656 ENSG00000093072 ENST00000262607.3 TRUE c.1082-656G>A p.= {"coding_transcript_intron_variant"} 656 +GRCh37 22 22 17664346 17664346 719 C CT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":11,"""dp""":11,"""gq""":32},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":10,"""gq""":41},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":12,"""gq""":63}} 1 0 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.248015 618 2262 0 51816 NM_017424.2 TRUE c.1082-696_1082-695insA p.= {"coding_transcript_intron_variant"} 695 ENSG00000093072 ENST00000262607.3 TRUE c.1082-696_1082-695insA p.= {"coding_transcript_intron_variant"} 695 +GRCh37 22 22 17664556 17664556 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":50,"""dp""":50,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":24,"""dp""":24,"""gq""":72},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 3 0 0 0 0 TRUE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.88613 12103 3163 0 51816 NM_017424.2 TRUE c.1082-905G>A p.= {"coding_transcript_intron_variant"} 905 ENSG00000093072 ENST00000262607.3 TRUE c.1082-905G>A p.= {"coding_transcript_intron_variant"} 905 +GRCh37 22 22 17664788 17664788 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":20,"""dp""":20,"""gq""":60}} 3 0 0 0 0 TRUE 0 0 0 0 0.879165 1947 486 0 0 0 0 0 0.887927 12185 3122 0 51816 NM_017424.2 TRUE c.1082-1137T>C p.= {"coding_transcript_intron_variant"} 1137 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1137T>C p.= {"coding_transcript_intron_variant"} 1137 +GRCh37 22 22 17664845 17664845 719 C CTT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":4,"""gq""":12},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":5,"""dp""":12,"""gq""":61},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":2,"""dp""":2,"""gq""":6}} 1 1 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.1082-1195_1082-1194insAA p.= {"coding_transcript_intron_variant"} 1194 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1195_1082-1194insAA p.= {"coding_transcript_intron_variant"} 1194 +GRCh37 22 22 17664845 17664845 719 C CTTT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":4,"""dp""":4,"""gq""":12},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":12,"""gq""":61},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":2,"""gq""":6}} 1 1 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.1082-1195_1082-1194insAAA p.= {"coding_transcript_intron_variant"} 1194 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1195_1082-1194insAAA p.= {"coding_transcript_intron_variant"} 1194 +GRCh37 22 22 17665080 17665080 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.885834 11962 3140 0 51816 NM_017424.2 TRUE c.1082-1429T>C p.= {"coding_transcript_intron_variant"} 1429 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1429T>C p.= {"coding_transcript_intron_variant"} 1429 +GRCh37 22 22 17665144 17665144 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.886295 12226 3188 0 51816 NM_017424.2 TRUE c.1082-1493T>C p.= {"coding_transcript_intron_variant"} 1493 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1493T>C p.= {"coding_transcript_intron_variant"} 1493 +GRCh37 22 22 17665413 17665413 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.885869 12280 3212 0 51816 NM_017424.2 TRUE c.1082-1762A>G p.= {"coding_transcript_intron_variant"} 1762 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1762A>G p.= {"coding_transcript_intron_variant"} 1762 +GRCh37 22 22 17665661 17665661 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":18,"""dp""":18,"""gq""":54},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":19,"""dp""":19,"""gq""":57},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.885306 11893 3122 0 51816 NM_017424.2 TRUE c.1082-2010T>G p.= {"coding_transcript_intron_variant"} 2010 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2010T>G p.= {"coding_transcript_intron_variant"} 2010 +GRCh37 22 22 17665782 17665838 719 ACACTCTAGCCTGGGTGACAGAGGTGGAGGCTGTAGTGAGCTGTCATCACACCACCG A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":16,"""dp""":16,"""gq""":49},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":18,"""dp""":18,"""gq""":57},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":17,"""dp""":17,"""gq""":55}} 3 0 0 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.834212 7994 2373 0 51816 NM_017424.2 TRUE c.1082-2187_1082-2132del p.= {"coding_transcript_intron_variant"} 2131 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2187_1082-2132del p.= {"coding_transcript_intron_variant"} 2131 +GRCh37 22 22 17665873 17665873 719 A AATATATATATATATATATATATATATATAT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":3,"""dp""":3,"""gq""":13},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":6,"""dp""":17,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":0,"""dp""":17,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.1082-2223_1082-2222insATATATATATATATATATATATATATATAT p.= {"coding_transcript_intron_variant"} 2222 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2223_1082-2222insATATATATATATATATATATATATATATAT p.= {"coding_transcript_intron_variant"} 2222 +GRCh37 22 22 17666164 17666164 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":25,"""gq""":74},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":39,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.886538 11936 3116 0 51816 NM_017424.2 TRUE c.1082-2513G>A p.= {"coding_transcript_intron_variant"} 2513 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2513G>A p.= {"coding_transcript_intron_variant"} 2513 +GRCh37 22 22 17666223 17666223 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":26,"""gq""":78},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.886468 12171 3158 0 51816 NM_017424.2 TRUE c.1082-2572C>T p.= {"coding_transcript_intron_variant"} 2572 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2572C>T p.= {"coding_transcript_intron_variant"} 2572 +GRCh37 22 22 17666279 17666279 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":29,"""gq""":87},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":45,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.272381 286 785 0 0 0 0 0 0.222927 1004 4876 0 51816 NM_017424.2 TRUE c.1082-2628G>A p.= {"coding_transcript_intron_variant"} 2628 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2628G>A p.= {"coding_transcript_intron_variant"} 2628 +GRCh37 22 22 17666280 17666280 719 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.876556 1935 497 0 0 0 0 0 0.88578 12161 3185 0 51816 NM_017424.2 TRUE c.1082-2629A>C p.= {"coding_transcript_intron_variant"} 2629 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2629A>C p.= {"coding_transcript_intron_variant"} 2629 +GRCh37 22 22 17666306 17666316 719 AAAAATAAAAT A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":22,"""dp""":22,"""gq""":67},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":24,"""dp""":24,"""gq""":73},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":91}} 3 0 0 0 0 FALSE 0 0 0 0 0.876957 1937 495 0 0 0 0 0 0.883708 11647 3090 0 51816 NM_017424.2 TRUE c.1082-2665_1082-2656del p.= {"coding_transcript_intron_variant"} 2655 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2665_1082-2656del p.= {"coding_transcript_intron_variant"} 2655 +GRCh37 22 22 17666437 17666437 719 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.87776 1940 493 0 0 0 0 0 0.885891 12281 3216 0 51816 NM_017424.2 TRUE c.1082-2786T>A p.= {"coding_transcript_intron_variant"} 2786 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2786T>A p.= {"coding_transcript_intron_variant"} 2786 +GRCh37 22 22 17666702 17666702 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.879366 1947 487 0 0 0 0 0 0.883223 12122 3279 0 51816 NM_017424.2 TRUE c.1081+2527A>G p.= {"coding_transcript_intron_variant"} 2527 ENSG00000093072 ENST00000262607.3 TRUE c.1081+2527A>G p.= {"coding_transcript_intron_variant"} 2527 +GRCh37 22 22 17666725 17666725 719 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":44,"""dp""":44,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.879566 1948 486 0 0 0 0 0 0.8836 12122 3266 0 51816 NM_017424.2 TRUE c.1081+2504A>C p.= {"coding_transcript_intron_variant"} 2504 ENSG00000093072 ENST00000262607.3 TRUE c.1081+2504A>C p.= {"coding_transcript_intron_variant"} 2504 +GRCh37 22 22 17666727 17666727 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.878964 1945 489 0 0 0 0 0 0.883585 12119 3268 0 51816 NM_017424.2 TRUE c.1081+2502A>G p.= {"coding_transcript_intron_variant"} 2502 ENSG00000093072 ENST00000262607.3 TRUE c.1081+2502A>G p.= {"coding_transcript_intron_variant"} 2502 +GRCh37 22 22 17667279 17667280 719 TG T indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 1.0 15689 0 0 51816 NM_017424.2 TRUE c.1081+1949del p.= {"coding_transcript_intron_variant"} 1949 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1949del p.= {"coding_transcript_intron_variant"} 1949 +GRCh37 22 22 17667426 17667426 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":39,"""gq""":91},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.624448 1027 1057 0 0 0 0 0 0.640303 6414 7047 0 51816 NM_017424.2 TRUE c.1081+1803G>A p.= {"coding_transcript_intron_variant"} 1803 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1803G>A p.= {"coding_transcript_intron_variant"} 1803 +GRCh37 22 22 17667451 17667451 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.880369 1953 480 0 0 0 0 0 0.884468 12030 3217 0 51816 NM_017424.2 TRUE c.1081+1778C>T p.= {"coding_transcript_intron_variant"} 1778 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1778C>T p.= {"coding_transcript_intron_variant"} 1778 +GRCh37 22 22 17667466 17667466 719 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.880169 1952 481 0 0 0 0 0 0.888268 12164 3171 0 51816 NM_017424.2 TRUE c.1081+1763A>T p.= {"coding_transcript_intron_variant"} 1763 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1763A>T p.= {"coding_transcript_intron_variant"} 1763 +GRCh37 22 22 17667737 17667737 719 T TGACA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":90}} 3 0 0 0 0 FALSE 0 0 0 0 0.877559 1940 492 0 0 0 0 0 0.885101 11864 3172 0 51816 NM_017424.2 TRUE c.1081+1491_1081+1492insTGTC p.= {"coding_transcript_intron_variant"} 1492 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1491_1081+1492insTGTC p.= {"coding_transcript_intron_variant"} 1492 +GRCh37 22 22 17668056 17668056 719 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":27,"""gq""":58},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":26,"""gq""":56},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":80}} 3 0 0 0 0 FALSE 0 0 0 0 0.503011 526 1454 0 0 0 0 0 0.699943 4996 4851 0 51816 NM_017424.2 TRUE c.1081+1172_1081+1173insT p.= {"coding_transcript_intron_variant"} 1173 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1172_1081+1173insT p.= {"coding_transcript_intron_variant"} 1173 +GRCh37 22 22 17668491 17668491 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":88},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":50,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.315737 313 947 0 0 0 0 0 0.264337 1192 5719 0 51816 NM_017424.2 TRUE c.1081+738G>A p.= {"coding_transcript_intron_variant"} 738 ENSG00000093072 ENST00000262607.3 TRUE c.1081+738G>A p.= {"coding_transcript_intron_variant"} 738 +GRCh37 22 22 17668568 17668568 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":50,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.267162 271 789 0 0 0 0 0 0.212419 902 4569 0 51816 NM_017424.2 TRUE c.1081+661T>C p.= {"coding_transcript_intron_variant"} 661 ENSG00000093072 ENST00000262607.3 TRUE c.1081+661T>C p.= {"coding_transcript_intron_variant"} 661 +GRCh37 22 22 17668765 17668765 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":31,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.195905 114 748 0 0 0 0 0 0.276868 1238 6077 0 51816 NM_017424.2 TRUE c.1081+464T>G p.= {"coding_transcript_intron_variant"} 464 ENSG00000093072 ENST00000262607.3 TRUE c.1081+464T>G p.= {"coding_transcript_intron_variant"} 464 +GRCh37 22 22 17668850 17668850 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":31,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":49,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.192894 116 729 0 0 0 0 0 0.272075 1157 6030 0 51816 NM_017424.2 TRUE c.1081+379G>A p.= {"coding_transcript_intron_variant"} 379 ENSG00000093072 ENST00000262607.3 TRUE c.1081+379G>A p.= {"coding_transcript_intron_variant"} 379 +GRCh37 22 22 17668851 17668851 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":32,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":49,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.196708 118 744 0 0 0 0 0 0.275662 1171 6112 0 51816 NM_017424.2 TRUE c.1081+378T>C p.= {"coding_transcript_intron_variant"} 378 ENSG00000093072 ENST00000262607.3 TRUE c.1081+378T>C p.= {"coding_transcript_intron_variant"} 378 +GRCh37 22 22 17668983 17668983 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":31,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.571457 772 1303 0 0 0 0 0 0.552056 4490 6917 0 51816 NM_017424.2 TRUE c.1081+246C>T p.= {"coding_transcript_intron_variant"} 246 ENSG00000093072 ENST00000262607.3 TRUE c.1081+246C>T p.= {"coding_transcript_intron_variant"} 246 +GRCh37 22 22 17668992 17668994 719 GAA G indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":34,"""gq""":99}} 1 0 2 0 0 TRUE 0 0 0 0 0.60277 949 1105 0 0 0 0 0 0.555981 4605 6909 0 51816 NM_017424.2 TRUE c.1081+235_1081+236del p.= {"coding_transcript_intron_variant"} 235 ENSG00000093072 ENST00000262607.3 TRUE c.1081+235_1081+236del p.= {"coding_transcript_intron_variant"} 235 +GRCh37 22 22 17669151 17669151 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":47,"""gq""":99}} 1 1 1 0 0 TRUE 0 0 0 0 0.675231 1184 996 0 0 0 0 0 0.672399 7122 6829 0 51816 NM_017424.2 TRUE c.1081+78G>A p.= {"coding_transcript_intron_variant"} 78 ENSG00000093072 ENST00000262607.3 TRUE c.1081+78G>A p.= {"coding_transcript_intron_variant"} 78 +GRCh37 22 22 17669406 17669406 719 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":36,"""gq""":99}} 1 0 2 0 0 TRUE 0 0 0 0 0.562425 866 1070 0 0 0 0 0 0.683436 7504 6348 0 51816 NM_017424.2 TRUE c.973-69C>G p.= {"coding_transcript_intron_variant"} 69 ENSG00000093072 ENST00000262607.3 TRUE c.973-69C>G p.= {"coding_transcript_intron_variant"} 69 +GRCh37 22 22 17669469 17669469 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":36,"""gq""":99}} 0 1 2 0 0 TRUE 0 0 0 0 0.278202 228 930 0 0 0 0 0 0.344286 1908 6903 0 51816 NM_017424.2 TRUE c.973-132A>G p.= {"coding_transcript_intron_variant"} 132 ENSG00000093072 ENST00000262607.3 TRUE c.973-132A>G p.= {"coding_transcript_intron_variant"} 132 +GRCh37 22 22 17669686 17669686 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":15,"""dp""":15,"""gq""":45},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":14,"""dp""":14,"""gq""":42},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":18,"""dp""":18,"""gq""":54}} 3 0 0 0 0 FALSE 0 0 0 0 0.804295 1639 729 0 0 0 0 0 0.809164 8833 3984 0 51816 NM_017424.2 TRUE c.973-349T>C p.= {"coding_transcript_intron_variant"} 349 ENSG00000093072 ENST00000262607.3 TRUE c.973-349T>C p.= {"coding_transcript_intron_variant"} 349 +GRCh37 22 22 17669760 17669760 719 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":9,"""dp""":9,"""gq""":27},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":6,"""dp""":12,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":13,"""gq""":39}} 1 1 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.299566 320 1155 0 51816 NM_017424.2 TRUE c.973-423A>T p.= {"coding_transcript_intron_variant"} 423 ENSG00000093072 ENST00000262607.3 TRUE c.973-423A>T p.= {"coding_transcript_intron_variant"} 423 +GRCh37 22 22 17669870 17669870 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":31,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.781614 1559 776 0 0 0 0 0 0.782287 8598 4453 0 51816 NM_017424.2 TRUE c.973-533T>C p.= {"coding_transcript_intron_variant"} 533 ENSG00000093072 ENST00000262607.3 TRUE c.973-533T>C p.= {"coding_transcript_intron_variant"} 533 +GRCh37 22 22 17669896 17669896 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":26,"""gq""":78},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.815134 1670 721 0 0 0 0 0 0.817912 9150 4047 0 51816 NM_017424.2 TRUE c.973-559T>G p.= {"coding_transcript_intron_variant"} 559 ENSG00000093072 ENST00000262607.3 TRUE c.973-559T>G p.= {"coding_transcript_intron_variant"} 559 +GRCh37 22 22 17669909 17669911 719 CTT C indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":15,"""dp""":15,"""gq""":45},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":20,"""dp""":20,"""gq""":60},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":17,"""dp""":18,"""gq""":33}} 3 0 0 0 0 FALSE 0 0 0 0 0.7222 1290 1018 0 0 0 0 0 0.473669 1512 3596 0 51816 NM_017424.2 TRUE c.973-574_973-573del p.= {"coding_transcript_intron_variant"} 572 ENSG00000093072 ENST00000262607.3 TRUE c.973-574_973-573del p.= {"coding_transcript_intron_variant"} 572 +GRCh37 22 22 17670256 17670256 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.613007 972 1110 0 0 0 0 0 0.574891 5196 7563 0 51816 NM_017424.2 TRUE c.972+576G>A p.= {"coding_transcript_intron_variant"} 576 ENSG00000093072 ENST00000262607.3 TRUE c.972+576G>A p.= {"coding_transcript_intron_variant"} 576 +GRCh37 22 22 17671133 17671133 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":51,"""dp""":51,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.481333 618 1162 0 0 0 0 0 0.489595 3794 7752 0 51816 NM_017424.2 TRUE c.882-211G>C p.= {"coding_transcript_intron_variant"} 211 ENSG00000093072 ENST00000262607.3 TRUE c.882-211G>C p.= {"coding_transcript_intron_variant"} 211 +GRCh37 22 22 17673165 17673165 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":31,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 1.0 15686 0 0 51816 NM_017424.2 TRUE c.754-465T>G p.= {"coding_transcript_intron_variant"} 465 ENSG00000093072 ENST00000262607.3 TRUE c.754-465T>G p.= {"coding_transcript_intron_variant"} 465 +GRCh37 22 22 17673719 17673720 719 GA G indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":28,"""dp""":28,"""gq""":84}} 3 0 0 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.536169 3709 7391 0 51816 NM_017424.2 TRUE c.754-1020del p.= {"coding_transcript_intron_variant"} 1019 ENSG00000093072 ENST00000262607.3 TRUE c.754-1020del p.= {"coding_transcript_intron_variant"} 1019 +GRCh37 22 22 17674248 17674250 719 CAA C indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":5,"""gq""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":7,"""gq""":37},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":6,"""dp""":10,"""gq""":48}} 0 1 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.0539568 24 492 0 51816 NM_017424.2 TRUE c.754-1550_754-1549del p.= {"coding_transcript_intron_variant"} 1548 ENSG00000093072 ENST00000262607.3 TRUE c.754-1550_754-1549del p.= {"coding_transcript_intron_variant"} 1548 +GRCh37 22 22 17674248 17674249 719 CA C indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":5,"""gq""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":3,"""dp""":7,"""gq""":37},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":10,"""gq""":48}} 0 0 3 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.028777 11 266 0 51816 NM_017424.2 TRUE c.754-1550del p.= {"coding_transcript_intron_variant"} 1548 ENSG00000093072 ENST00000262607.3 TRUE c.754-1550del p.= {"coding_transcript_intron_variant"} 1548 +GRCh37 22 22 17674568 17674568 719 T TA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":24,"""dp""":24,"""gq""":71},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":28,"""gq""":55},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.569394 3193 6168 0 51816 NM_017424.2 TRUE c.754-1869_754-1868insT p.= {"coding_transcript_intron_variant"} 1868 ENSG00000093072 ENST00000262607.3 TRUE c.754-1869_754-1868insT p.= {"coding_transcript_intron_variant"} 1868 +GRCh37 22 22 17674909 17674909 719 G GA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":20,"""gq""":60},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":9,"""dp""":19,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":10,"""dp""":24,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.530227 2379 5416 0 51816 NM_017424.2 TRUE c.754-2210_754-2209insT p.= {"coding_transcript_intron_variant"} 2209 ENSG00000093072 ENST00000262607.3 TRUE c.754-2210_754-2209insT p.= {"coding_transcript_intron_variant"} 2209 +GRCh37 22 22 17675900 17675900 719 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.541148 794 1108 0 0 0 0 0 0.448263 3311 7388 0 51816 NM_017424.2 TRUE c.754-3200G>T p.= {"coding_transcript_intron_variant"} 3200 ENSG00000093072 ENST00000262607.3 TRUE c.754-3200G>T p.= {"coding_transcript_intron_variant"} 3200 +GRCh37 22 22 17676102 17676102 719 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":54,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.557407 833 1111 0 0 0 0 0 0.490608 3901 7555 0 51816 NM_017424.2 TRUE c.754-3402A>T p.= {"coding_transcript_intron_variant"} 3402 ENSG00000093072 ENST00000262607.3 TRUE c.754-3402A>T p.= {"coding_transcript_intron_variant"} 3402 +GRCh37 22 22 17676410 17676410 719 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.637696 1069 1039 0 0 0 0 0 0.521741 4181 7189 0 51816 NM_017424.2 TRUE c.754-3710G>T p.= {"coding_transcript_intron_variant"} 3710 ENSG00000093072 ENST00000262607.3 TRUE c.754-3710G>T p.= {"coding_transcript_intron_variant"} 3710 +GRCh37 22 22 17676414 17676414 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.637495 1068 1040 0 0 0 0 0 0.522792 4173 7160 0 51816 NM_017424.2 TRUE c.754-3714C>T p.= {"coding_transcript_intron_variant"} 3714 ENSG00000093072 ENST00000262607.3 TRUE c.754-3714C>T p.= {"coding_transcript_intron_variant"} 3714 +GRCh37 22 22 17676418 17676418 719 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.523485 581 1446 0 0 0 0 0 0.522123 3994 7140 0 51816 NM_017424.2 TRUE c.754-3719_754-3718insT p.= {"coding_transcript_intron_variant"} 3718 ENSG00000093072 ENST00000262607.3 TRUE c.754-3719_754-3718insT p.= {"coding_transcript_intron_variant"} 3718 +GRCh37 22 22 17676590 17676590 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.134083 59 550 0 0 0 0 0 0.139134 349 3589 0 51816 NM_017424.2 TRUE c.754-3890T>C p.= {"coding_transcript_intron_variant"} 3890 ENSG00000093072 ENST00000262607.3 TRUE c.754-3890T>C p.= {"coding_transcript_intron_variant"} 3890 +GRCh37 22 22 17676604 17676604 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":50,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.00200723 0 10 0 0 0 0 0 0.00453427 2 136 0 51816 NM_017424.2 TRUE c.754-3904A>G p.= {"coding_transcript_intron_variant"} 3904 ENSG00000093072 ENST00000262607.3 TRUE c.754-3904A>G p.= {"coding_transcript_intron_variant"} 3904 +GRCh37 22 22 17676785 17676785 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":98}} 1 0 2 0 0 FALSE 0 0 0 0 0.721999 1349 899 0 0 0 0 0 0.591954 5687 6960 0 51816 NM_017424.2 TRUE c.754-4085T>C p.= {"coding_transcript_intron_variant"} 4085 ENSG00000093072 ENST00000262607.3 TRUE c.754-4085T>C p.= {"coding_transcript_intron_variant"} 4085 +GRCh37 22 22 17677175 17677175 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":29,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":21,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":90}} 1 0 2 0 0 FALSE 0 0 0 0 0.274789 193 983 0 0 0 0 0 0.235866 872 5223 0 51816 NM_017424.2 TRUE c.754-4475A>G p.= {"coding_transcript_intron_variant"} 4475 ENSG00000093072 ENST00000262607.3 TRUE c.754-4475A>G p.= {"coding_transcript_intron_variant"} 4475 +GRCh37 22 22 17677213 17677213 719 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":26,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":15,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":22,"""dp""":22,"""gq""":66}} 1 0 2 0 0 FALSE 0 0 0 0 0.182658 89 732 0 0 0 0 0 0.387504 757 3336 0 51816 NM_017424.2 TRUE c.754-4514_754-4513insT p.= {"coding_transcript_intron_variant"} 4513 ENSG00000093072 ENST00000262607.3 TRUE c.754-4514_754-4513insT p.= {"coding_transcript_intron_variant"} 4513 +GRCh37 22 22 17677321 17677321 719 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":45,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 2.00723E-4 0 1 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.754-4621A>C p.= {"coding_transcript_intron_variant"} 4621 ENSG00000093072 ENST00000262607.3 TRUE c.754-4621A>C p.= {"coding_transcript_intron_variant"} 4621 +GRCh37 22 22 17677699 17677699 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.70273 1269 963 0 0 0 0 0 0.585983 5605 7143 0 51816 NM_017424.2 TRUE c.754-4999G>A p.= {"coding_transcript_intron_variant"} 4999 ENSG00000093072 ENST00000262607.3 TRUE c.754-4999G>A p.= {"coding_transcript_intron_variant"} 4999 +GRCh37 22 22 17678128 17678128 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.714572 1308 944 0 0 0 0 0 0.596935 5779 6947 0 51816 NM_017424.2 TRUE c.754-5428G>C p.= {"coding_transcript_intron_variant"} 5428 ENSG00000093072 ENST00000262607.3 TRUE c.754-5428G>C p.= {"coding_transcript_intron_variant"} 5428 +GRCh37 22 22 17678159 17678159 719 C CT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":29,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.170413 58 733 0 0 0 0 0 0.188241 432 3868 0 51816 NM_017424.2 TRUE c.754-5460_754-5459insA p.= {"coding_transcript_intron_variant"} 5459 ENSG00000093072 ENST00000262607.3 TRUE c.754-5460_754-5459insA p.= {"coding_transcript_intron_variant"} 5459 +GRCh37 22 22 17678195 17678195 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.253713 180 904 0 0 0 0 0 0.235237 879 5269 0 51816 NM_017424.2 TRUE c.754-5495G>A p.= {"coding_transcript_intron_variant"} 5495 ENSG00000093072 ENST00000262607.3 TRUE c.754-5495G>A p.= {"coding_transcript_intron_variant"} 5495 diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz deleted file mode 120000 index e1c8033..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz new file mode 100644 index 0000000..74cfa06 Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz differ diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz.tbi deleted file mode 120000 index 295a488..0000000 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz.tbi +++ /dev/null @@ -1 +0,0 @@ -../../../../../../tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz.tbi \ No newline at end of file diff --git a/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz.tbi b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz.tbi new file mode 100644 index 0000000..d96f5df Binary files /dev/null and b/varfish-annotator-cli/src/test/resources/input/grch37-chr22/Case_1_index.gatk_hc.vcf.gz.tbi differ diff --git a/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.cnv.gts.tsv b/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.cnv.gts.tsv index 6334f68..f827138 100644 --- a/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.cnv.gts.tsv +++ b/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.cnv.gts.tsv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:31f50efc3eb4bc13b1f5e40bde68561bf91b86e26971d3832ef9e59ea72c9951 +oid sha256:dcaf75b3f01839efe836d4c66ee0f391d5cf97a24e982c90d86c6c5064bb9728 size 162863 diff --git a/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.sv.gts.tsv b/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.sv.gts.tsv index fdd87f5..2cbbc98 100644 --- a/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.sv.gts.tsv +++ b/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragen.sv.gts.tsv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:714dc98ae59d15dabf01366f4242c5410e5b432905c333bc2949109f1360f643 +oid sha256:9d197e6bcc4e1a222f2d82a619a52de0d8ce4b4da01be26a505bac0884fe0966 size 2621930 diff --git a/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.delly2.Case_1_index-N1-DNA1-WGS1.gts.tsv b/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.delly2.Case_1_index-N1-DNA1-WGS1.gts.tsv index 7f9f728..13904ea 100644 --- a/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.delly2.Case_1_index-N1-DNA1-WGS1.gts.tsv +++ b/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.delly2.Case_1_index-N1-DNA1-WGS1.gts.tsv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:22b6ba1df1e083c28e7f8168157ba998864eb03149b2178900b4aa227bf595d8 +oid sha256:32592801e92a602524cb86074a0f5f45a03cad1d2336a87bb02419ed946f995c size 19498392 diff --git a/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.gcnv.NA12878-N1-DNA1-WGS1.gts.tsv b/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.gcnv.NA12878-N1-DNA1-WGS1.gts.tsv index c05f0c7..0103124 100644 --- a/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.gcnv.NA12878-N1-DNA1-WGS1.gts.tsv +++ b/varfish-annotator-cli/src/test/resources/input/real-world-37/bwa.gcnv.NA12878-N1-DNA1-WGS1.gts.tsv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:96311b8f376ab6ae66a53aedb6381cde5be1e39c1d41d5e7bcbce82b6f865708 +oid sha256:6021f39c4b2c147f9ebde4ca499ef5814a266c6e2c2974a6755bf2c35f384d46 size 160855 diff --git a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecord.java b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecord.java new file mode 100644 index 0000000..e270977 --- /dev/null +++ b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecord.java @@ -0,0 +1,455 @@ +package com.github.bihealth.varfish_annotator.annotate_svs; + +import static com.github.bihealth.varfish_annotator.utils.StringUtils.tripleQuote; + +import com.google.common.base.Joiner; +import com.google.common.base.Objects; +import com.google.common.collect.ImmutableList; +import com.google.common.collect.ImmutableMap; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +public class GenotypeRecord { + /** Header fields for the SV and genotype file (part 1). */ + private static final ImmutableList HEADERS_GT_PART_1 = + ImmutableList.of("release", "chromosome", "chromosome_no", "bin"); + /** Header fields for the SV and genotype file (part 2, optional). */ + private static final ImmutableList HEADERS_GT_PART_2 = + ImmutableList.of("chromosome2", "chromosome_no2", "bin2", "pe_orientation"); + /** Header fields for the SV and genotype file (part 3). */ + private static final ImmutableList HEADERS_GT_PART_3 = + ImmutableList.of( + "start", + "end", + "start_ci_left", + "start_ci_right", + "end_ci_left", + "end_ci_right", + "case_id", + "set_id", + "sv_uuid", + "caller", + "sv_type", + "sv_sub_type", + "info"); + /** Header fields for the SV and genotype file (part 4, optional). */ + private static final ImmutableList HEADERS_GT_PART_4 = + ImmutableList.of("num_hom_alt", "num_hom_ref", "num_het", "num_hemi_alt", "num_hemi_ref"); + /** Header fields for the SV and genotype file (part 5). */ + private static final ImmutableList HEADERS_GT_PART_5 = ImmutableList.of("genotype"); + + private final String release; + private final String chromosome; + private final int chromosomeNo; + private final int bin; + private final String chromosome2; + private final int chromosomeNo2; + private final int bin2; + private final String peOrientation; + private final int start; + private final int end; + private final int startCiLeft; + private final int startCiRight; + private final int endCiLeft; + private final int endCiRight; + private final String caseId; + private final String setId; + private final String svUuid; + private final String caller; + private final String svType; + private final String svSubType; + private final ImmutableMap info; + + private final int numHomAlt; + private final int numHomRef; + private final int numHet; + private final int numHemiAlt; + private final int numHemiRef; + private final ImmutableMap genotype; + + public GenotypeRecord( + String release, + String chromosome, + int chromosomeNo, + int bin, + String chromosome2, + int chromosomeNo2, + int bin2, + String peOrientation, + int start, + int end, + int startCiLeft, + int startCiRight, + int endCiLeft, + int endCiRight, + String caseId, + String setId, + String svUuid, + String caller, + String svType, + String svSubType, + Map info, + int numHomAlt, + int numHomRef, + int numHet, + int numHemiAlt, + int numHemiRef, + Map genotype) { + this.release = release; + this.chromosome = chromosome; + this.chromosomeNo = chromosomeNo; + this.bin = bin; + this.chromosome2 = chromosome2; + this.chromosomeNo2 = chromosomeNo2; + this.bin2 = bin2; + this.peOrientation = peOrientation; + this.start = start; + this.end = end; + this.startCiLeft = startCiLeft; + this.startCiRight = startCiRight; + this.endCiLeft = endCiLeft; + this.endCiRight = endCiRight; + this.caseId = caseId; + this.setId = setId; + this.svUuid = svUuid; + this.caller = caller; + this.svType = svType; + this.svSubType = svSubType; + this.info = ImmutableMap.copyOf(info); + this.numHomAlt = numHomAlt; + this.numHomRef = numHomRef; + this.numHet = numHet; + this.numHemiAlt = numHemiAlt; + this.numHemiRef = numHemiRef; + this.genotype = ImmutableMap.copyOf(genotype); + } + + public static String tsvHeader(boolean showChrom2Columns, boolean showDbCountColumns) { + // (Conditionally) write genotype header. + final List headers = new ArrayList<>(); + headers.addAll(HEADERS_GT_PART_1); + if (showChrom2Columns) { + headers.addAll(HEADERS_GT_PART_2); + } + headers.addAll(HEADERS_GT_PART_3); + if (showDbCountColumns) { + headers.addAll(HEADERS_GT_PART_4); + } + headers.addAll(HEADERS_GT_PART_5); + return Joiner.on("\t").join(headers); + } + + public String toTsv(boolean showChrom2Columns, boolean showDbCountColumns) { + final ImmutableList.Builder builder = ImmutableList.builder(); + builder.add(release, chromosome, chromosomeNo, bin); + if (showChrom2Columns) { + builder.add(chromosome2, chromosomeNo2, bin2, peOrientation); + } + builder.add( + start, + end, + startCiLeft, + startCiRight, + endCiLeft, + endCiRight, + caseId, + setId, + svUuid, + caller, + svType, + svSubType); + builder.add(convert(info)); + if (showDbCountColumns) { + builder.add(numHomAlt, numHomRef, numHet, numHemiAlt, numHemiRef); + } + builder.add(convert(genotype)); + return Joiner.on("\t").useForNull(".").join(builder.build()); + } + + private String convert(Object value) { + final ImmutableList.Builder innerBuilder = ImmutableList.builder(); + pushValue(value, innerBuilder); + return Joiner.on("").useForNull(".").join(innerBuilder.build()); + } + + private void pushValue(Object value, ImmutableList.Builder builder) { + if (value instanceof Integer || value instanceof Double || value instanceof Float) { + builder.add(value.toString()); + } else if (value instanceof String) { + builder.add(tripleQuote(value.toString())); + } else if (value instanceof List) { + final List valueAsList = (List) value; + builder.add("{"); + boolean first = true; + for (Object element : valueAsList) { + if (!first) { + builder.add(","); + } + pushValue(element, builder); + first = false; + } + builder.add("}"); + } else if (value instanceof Map) { + final Map valueAsMap = (Map) value; + builder.add("{"); + boolean first = true; + for (String key : valueAsMap.keySet()) { + if (!first) { + builder.add(","); + } + pushValue(key, builder); + builder.add(":"); + pushValue(valueAsMap.get(key), builder); + first = false; + } + builder.add("}"); + } else { + throw new RuntimeException("Could not encode " + value); + } + } + + public String getRelease() { + return release; + } + + public String getChromosome() { + return chromosome; + } + + public int getChromosomeNo() { + return chromosomeNo; + } + + public int getBin() { + return bin; + } + + public String getChromosome2() { + return chromosome2; + } + + public int getChromosomeNo2() { + return chromosomeNo2; + } + + public int getBin2() { + return bin2; + } + + public String getPeOrientation() { + return peOrientation; + } + + public int getStart() { + return start; + } + + public int getEnd() { + return end; + } + + public int getStartCiLeft() { + return startCiLeft; + } + + public int getStartCiRight() { + return startCiRight; + } + + public int getEndCiLeft() { + return endCiLeft; + } + + public int getEndCiRight() { + return endCiRight; + } + + public String getCaseId() { + return caseId; + } + + public String getSetId() { + return setId; + } + + public String getSvUuid() { + return svUuid; + } + + public String getCaller() { + return caller; + } + + public String getSvType() { + return svType; + } + + public String getSvSubType() { + return svSubType; + } + + public ImmutableMap getInfo() { + return info; + } + + public int getNumHomAlt() { + return numHomAlt; + } + + public int getNumHomRef() { + return numHomRef; + } + + public int getNumHet() { + return numHet; + } + + public int getNumHemiAlt() { + return numHemiAlt; + } + + public int getNumHemiRef() { + return numHemiRef; + } + + public ImmutableMap getGenotype() { + return genotype; + } + + @Override + public String toString() { + return "GenotypeRecord{" + + "release='" + + release + + '\'' + + ", chromosome='" + + chromosome + + '\'' + + ", chromosomeNo=" + + chromosomeNo + + ", bin=" + + bin + + ", chromosome2='" + + chromosome2 + + '\'' + + ", chromosomeNo2=" + + chromosomeNo2 + + ", bin2=" + + bin2 + + ", peOrientation='" + + peOrientation + + '\'' + + ", start=" + + start + + ", end=" + + end + + ", startCiLeft=" + + startCiLeft + + ", startCiRight=" + + startCiRight + + ", endCiLeft=" + + endCiLeft + + ", endCiRight=" + + endCiRight + + ", caseId='" + + caseId + + '\'' + + ", setId='" + + setId + + '\'' + + ", svUuid='" + + svUuid + + '\'' + + ", caller='" + + caller + + '\'' + + ", svType='" + + svType + + '\'' + + ", svSubType='" + + svSubType + + '\'' + + ", info=" + + info + + ", numHomAlt=" + + numHomAlt + + ", numHomRef=" + + numHomRef + + ", numHet=" + + numHet + + ", numHemiAlt=" + + numHemiAlt + + ", numHemiRef=" + + numHemiRef + + ", genotype=" + + genotype + + '}'; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + GenotypeRecord that = (GenotypeRecord) o; + return getChromosomeNo() == that.getChromosomeNo() + && getBin() == that.getBin() + && getChromosomeNo2() == that.getChromosomeNo2() + && getBin2() == that.getBin2() + && getStart() == that.getStart() + && getEnd() == that.getEnd() + && getStartCiLeft() == that.getStartCiLeft() + && getStartCiRight() == that.getStartCiRight() + && getEndCiLeft() == that.getEndCiLeft() + && getEndCiRight() == that.getEndCiRight() + && numHomAlt == that.numHomAlt + && numHomRef == that.numHomRef + && numHet == that.numHet + && numHemiAlt == that.numHemiAlt + && numHemiRef == that.numHemiRef + && Objects.equal(getRelease(), that.getRelease()) + && Objects.equal(getChromosome(), that.getChromosome()) + && Objects.equal(getChromosome2(), that.getChromosome2()) + && Objects.equal(getPeOrientation(), that.getPeOrientation()) + && Objects.equal(getCaseId(), that.getCaseId()) + && Objects.equal(getSetId(), that.getSetId()) + && Objects.equal(getSvUuid(), that.getSvUuid()) + && Objects.equal(getCaller(), that.getCaller()) + && Objects.equal(getSvType(), that.getSvType()) + && Objects.equal(getSvSubType(), that.getSvSubType()) + && Objects.equal(getInfo(), that.getInfo()) + && Objects.equal(genotype, that.genotype); + } + + @Override + public int hashCode() { + return Objects.hashCode( + getRelease(), + getChromosome(), + getChromosomeNo(), + getBin(), + getChromosome2(), + getChromosomeNo2(), + getBin2(), + getPeOrientation(), + getStart(), + getEnd(), + getStartCiLeft(), + getStartCiRight(), + getEndCiLeft(), + getEndCiRight(), + getCaseId(), + getSetId(), + getSvUuid(), + getCaller(), + getSvType(), + getSvSubType(), + getInfo(), + numHomAlt, + numHomRef, + numHet, + numHemiAlt, + numHemiRef, + genotype); + } +} diff --git a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordBuilder.java b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordBuilder.java new file mode 100644 index 0000000..f4f14b9 --- /dev/null +++ b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordBuilder.java @@ -0,0 +1,355 @@ +package com.github.bihealth.varfish_annotator.annotate_svs; + +import java.util.Map; +import java.util.TreeMap; + +/** Helper for building {@code GenotypeRecord} objects. */ +public class GenotypeRecordBuilder { + private String release; + private String chromosome; + private int chromosomeNo; + private int bin; + private String chromosome2; + private int chromosomeNo2; + private int bin2; + private String peOrientation; + private int start; + private int end; + private int startCiLeft; + private int startCiRight; + private int endCiLeft; + private int endCiRight; + private String caseId; + private String setId; + private String svUuid; + private String caller; + private String svType; + private String svSubType; + private Map info = new TreeMap(); + + private int numHomAlt; + private int numHomRef; + private int numHet; + private int numHemiAlt; + private int numHemiRef; + private Map genotype = new TreeMap(); + + public GenotypeRecord build() { + return new GenotypeRecord( + release, + chromosome, + chromosomeNo, + bin, + chromosome2, + chromosomeNo2, + bin2, + peOrientation, + start, + end, + startCiLeft, + startCiRight, + endCiLeft, + endCiRight, + caseId, + setId, + svUuid, + caller, + svType, + svSubType, + info, + numHomAlt, + numHomRef, + numHet, + numHemiAlt, + numHemiRef, + genotype); + } + + public String getRelease() { + return release; + } + + public void setRelease(String release) { + this.release = release; + } + + public String getChromosome() { + return chromosome; + } + + public void setChromosome(String chromosome) { + this.chromosome = chromosome; + } + + public int getChromosomeNo() { + return chromosomeNo; + } + + public void setChromosomeNo(int chromosomeNo) { + this.chromosomeNo = chromosomeNo; + } + + public int getBin() { + return bin; + } + + public void setBin(int bin) { + this.bin = bin; + } + + public String getChromosome2() { + return chromosome2; + } + + public void setChromosome2(String chromosome2) { + this.chromosome2 = chromosome2; + } + + public int getChromosomeNo2() { + return chromosomeNo2; + } + + public void setChromosomeNo2(int chromosomeNo2) { + this.chromosomeNo2 = chromosomeNo2; + } + + public int getBin2() { + return bin2; + } + + public void setBin2(int bin2) { + this.bin2 = bin2; + } + + public String getPeOrientation() { + return peOrientation; + } + + public void setPeOrientation(String peOrientation) { + this.peOrientation = peOrientation; + } + + public int getStart() { + return start; + } + + public void setStart(int start) { + this.start = start; + } + + public int getEnd() { + return end; + } + + public void setEnd(int end) { + this.end = end; + } + + public int getStartCiLeft() { + return startCiLeft; + } + + public void setStartCiLeft(int startCiLeft) { + this.startCiLeft = startCiLeft; + } + + public int getStartCiRight() { + return startCiRight; + } + + public void setStartCiRight(int startCiRight) { + this.startCiRight = startCiRight; + } + + public int getEndCiLeft() { + return endCiLeft; + } + + public void setEndCiLeft(int endCiLeft) { + this.endCiLeft = endCiLeft; + } + + public int getEndCiRight() { + return endCiRight; + } + + public void setEndCiRight(int endCiRight) { + this.endCiRight = endCiRight; + } + + public String getCaseId() { + return caseId; + } + + public void setCaseId(String caseId) { + this.caseId = caseId; + } + + public String getSetId() { + return setId; + } + + public void setSetId(String setId) { + this.setId = setId; + } + + public String getSvUuid() { + return svUuid; + } + + public void setSvUuid(String svUuid) { + this.svUuid = svUuid; + } + + public String getCaller() { + return caller; + } + + public void setCaller(String caller) { + this.caller = caller; + } + + public String getSvType() { + return svType; + } + + public void setSvType(String svType) { + this.svType = svType; + } + + public String getSvSubType() { + return svSubType; + } + + public void setSvSubType(String svSubType) { + this.svSubType = svSubType; + } + + public Map getInfo() { + return info; + } + + public void setInfo(Map info) { + this.info = new TreeMap(); + this.info.putAll(info); + } + + public int getNumHomAlt() { + return numHomAlt; + } + + public void setNumHomAlt(int numHomAlt) { + this.numHomAlt = numHomAlt; + } + + public int getNumHomRef() { + return numHomRef; + } + + public void setNumHomRef(int numHomRef) { + this.numHomRef = numHomRef; + } + + public int getNumHet() { + return numHet; + } + + public void setNumHet(int numHet) { + this.numHet = numHet; + } + + public int getNumHemiAlt() { + return numHemiAlt; + } + + public void setNumHemiAlt(int numHemiAlt) { + this.numHemiAlt = numHemiAlt; + } + + public int getNumHemiRef() { + return numHemiRef; + } + + public void setNumHemiRef(int numHemiRef) { + this.numHemiRef = numHemiRef; + } + + public Map getGenotype() { + return genotype; + } + + public void setGenotype(Map genotype) { + this.genotype = new TreeMap(); + this.genotype.putAll(genotype); + } + + @Override + public String toString() { + return "GenotypeRecordBuilder{" + + "release='" + + release + + '\'' + + ", chromosome='" + + chromosome + + '\'' + + ", chromosomeNo=" + + chromosomeNo + + ", bin=" + + bin + + ", chromosome2='" + + chromosome2 + + '\'' + + ", chromosomeNo2=" + + chromosomeNo2 + + ", bin2=" + + bin2 + + ", peOrientation='" + + peOrientation + + '\'' + + ", start=" + + start + + ", end=" + + end + + ", startCiLeft=" + + startCiLeft + + ", startCiRight=" + + startCiRight + + ", endCiLeft=" + + endCiLeft + + ", endCiRight=" + + endCiRight + + ", caseId='" + + caseId + + '\'' + + ", setId='" + + setId + + '\'' + + ", svUuid='" + + svUuid + + '\'' + + ", caller='" + + caller + + '\'' + + ", svType='" + + svType + + '\'' + + ", svSubType='" + + svSubType + + '\'' + + ", info=" + + info + + ", numHomAlt=" + + numHomAlt + + ", numHomRef=" + + numHomRef + + ", numHet=" + + numHet + + ", numHemiAlt=" + + numHemiAlt + + ", numHemiRef=" + + numHemiRef + + ", genotype=" + + genotype + + '}'; + } +} diff --git a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GtRecordBuilder.java b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GtRecordBuilder.java index b69e1a0..ee1b745 100644 --- a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GtRecordBuilder.java +++ b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GtRecordBuilder.java @@ -7,7 +7,6 @@ import com.github.bihealth.varfish_annotator.utils.UcscBinning; import com.google.common.base.Joiner; import com.google.common.collect.ImmutableList; -import com.google.common.collect.Lists; import com.google.common.primitives.Ints; import de.charite.compbio.jannovar.pedigree.Pedigree; import de.charite.compbio.jannovar.reference.SVDescription; @@ -25,34 +24,6 @@ public class GtRecordBuilder { public static final String FEATURE_DBCOUNTS_COLUMNS = "dbcounts-columns"; public static final String FEATURE_SUPPRESS_CARRIER_COUNTS = "suppress-carriers-in-info"; - /** Header fields for the SV and genotype file (part 1). */ - private static final ImmutableList HEADERS_GT_PART_1 = - ImmutableList.of("release", "chromosome", "chromosome_no", "bin"); - /** Header fields for the SV and genotype file (part 2, optional). */ - private static final ImmutableList HEADERS_GT_PART_2 = - ImmutableList.of("chromosome2", "chromosome_no2", "bin2", "pe_orientation"); - /** Header fields for the SV and genotype file (part 3). */ - private static final ImmutableList HEADERS_GT_PART_3 = - ImmutableList.of( - "start", - "end", - "start_ci_left", - "start_ci_right", - "end_ci_left", - "end_ci_right", - "case_id", - "set_id", - "sv_uuid", - "caller", - "sv_type", - "sv_sub_type", - "info"); - /** Header fields for the SV and genotype file (part 4, optional). */ - private static final ImmutableList HEADERS_GT_PART_4 = - ImmutableList.of("num_hom_alt", "num_hom_ref", "num_het", "num_hemi_alt", "num_hemi_ref"); - /** Header fields for the SV and genotype file (part 5). */ - private static final ImmutableList HEADERS_GT_PART_5 = ImmutableList.of("genotype"); - private final String release; private final String defaultSvMethod; private final String optOutFeatures; @@ -78,22 +49,105 @@ public GtRecordBuilder( this.callerSupport = callerSupport; } - public List getHeaders() { - // (Conditionally) write genotype header. - final List headers = new ArrayList<>(); - headers.addAll(HEADERS_GT_PART_1); - if (!optOutFeatures.contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS)) { - headers.addAll(HEADERS_GT_PART_2); + public GenotypeRecord buildRecord( + UUID variantId, + SVGenomeVariant svGenomeVar, + VariantContext ctx, + GenomeVersion genomeVersion, + int alleleNo) { + final GenotypeRecordBuilder builder = new GenotypeRecordBuilder(); + + builder.setRelease(release); + builder.setChromosome( + (genomeVersion == GenomeVersion.HG19) + ? svGenomeVar.getChrName().replaceFirst("chr", "") + : svGenomeVar.getChrName()); + builder.setChromosomeNo(svGenomeVar.getChr()); + + builder.setChromosome2( + (genomeVersion == GenomeVersion.HG19) + ? svGenomeVar.getChr2Name().replaceFirst("chr", "") + : svGenomeVar.getChr2Name()); + builder.setChromosomeNo2(svGenomeVar.getChr2()); + + if (svGenomeVar.getType() == SVDescription.Type.BND) { + builder.setEnd(svGenomeVar.getPos() + 1); + builder.setBin(UcscBinning.getContainingBin(svGenomeVar.getPos(), svGenomeVar.getPos() + 1)); + builder.setBin2( + UcscBinning.getContainingBin(svGenomeVar.getPos() + 1, svGenomeVar.getPos() + 2)); + } else { + builder.setEnd(svGenomeVar.getPos2()); + final int pos2 = svGenomeVar.getPos2(); + final int bin = UcscBinning.getContainingBin(svGenomeVar.getPos(), pos2); + builder.setBin(bin); + builder.setBin2(bin); + } + + builder.setPeOrientation(getPeOrientation(ctx, svGenomeVar, alleleNo)); + builder.setStart(svGenomeVar.getPos() + 1); + builder.setStartCiLeft(svGenomeVar.getPosCILowerBound()); + builder.setStartCiRight(svGenomeVar.getPosCIUpperBound()); + builder.setEndCiLeft(svGenomeVar.getPos2CILowerBound()); + builder.setEndCiRight(svGenomeVar.getPos2CIUpperBound()); + + builder.setCaseId(caseId); + builder.setSetId(setId); + builder.setSvUuid(variantId.toString()); + + String svMethod = ctx.getCommonInfo().getAttributeAsString("SVMETHOD", null); + if (svMethod == null) { + svMethod = defaultSvMethod == null ? "." : defaultSvMethod; } - headers.addAll(HEADERS_GT_PART_3); - if (!optOutFeatures.contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS)) { - headers.addAll(HEADERS_GT_PART_4); + builder.setCaller(svMethod); + + builder.setSvType(svGenomeVar.getType().toString()); + builder.setSvSubType(svGenomeVar.getType().toString()); + + final TreeMap info = new TreeMap<>(); + if (!optOutFeatures.contains(FEATURE_DBCOUNTS_COLUMNS)) { + augmentInfoValue(ctx, genomeVersion, svGenomeVar, info); } - headers.addAll(HEADERS_GT_PART_5); - return headers; + builder.setInfo(info); + + final GenotypeCounts gtCounts = + GenotypeCounts.buildGenotypeCounts(ctx, alleleNo, pedigree, release); + builder.setNumHomAlt(gtCounts.numHomAlt); + builder.setNumHomRef(gtCounts.numHomRef); + builder.setNumHet(gtCounts.numHet); + builder.setNumHemiAlt(gtCounts.numHemiAlt); + builder.setNumHemiRef(gtCounts.numHemiRef); + + builder.setGenotype(buildGenotypeValue(ctx, alleleNo)); + + return builder.build(); } - public List buildRecord( + private String getPeOrientation(VariantContext ctx, SVGenomeVariant svGenomeVar, int alleleNo) { + if (svGenomeVar.getType() == SVDescription.Type.INV) { + return "3to3"; + } else if (svGenomeVar.getType() == SVDescription.Type.DUP) { + return "5to3"; + } else if (svGenomeVar.getType() == SVDescription.Type.DEL) { + return "3to5"; + } else if (svGenomeVar.getType() == SVDescription.Type.BND) { + final String altBases = ctx.getAlternateAllele(alleleNo - 1).getDisplayString(); + if (altBases.startsWith("[")) { + return "3to5"; + } else if (altBases.startsWith("]")) { + return "5to3"; + } else if (altBases.endsWith("[")) { + return "3to5"; + } else if (altBases.endsWith("]")) { + return "3to3"; + } else { + return "."; + } + } else { + return "."; + } + } + + public List buildRecordOld( UUID variantId, SVGenomeVariant svGenomeVar, VariantContext ctx, @@ -171,7 +225,7 @@ public List buildRecord( // TODO: improve type and sub type annotation! svGenomeVar.getType(), svGenomeVar.getType(), - buildInfoValue(ctx, genomeVersion, svGenomeVar, optOutFeatures)); + ""); // buildInfoValue(ctx, genomeVersion, svGenomeVar, optOutFeatures)); // optional part 4 if (!optOutFeatures.contains(FEATURE_DBCOUNTS_COLUMNS)) { final GenotypeCounts gtCounts = @@ -184,58 +238,37 @@ public List buildRecord( String.valueOf(gtCounts.numHemiRef)); } // part 5 - result.add(buildGenotypeValue(ctx, alleleNo)); + // result.add(buildGenotypeValue(ctx, alleleNo)); return result.build(); } - private static String buildInfoValue( + private static void augmentInfoValue( VariantContext ctx, GenomeVersion genomeVersion, SVGenomeVariant svGenomeVar, - String optOutFeatures) { - final List mappings = new ArrayList<>(); - - if (!optOutFeatures.contains(FEATURE_SUPPRESS_CARRIER_COUNTS)) { - if (svGenomeVar.getType() == SVDescription.Type.BND) { - final String contigName2 = - (genomeVersion == GenomeVersion.HG19) - ? svGenomeVar.getChr2Name().replaceFirst("chr", "") - : svGenomeVar.getChr2Name(); - - mappings.add(tripleQuote("chr2") + ":" + tripleQuote(contigName2)); - mappings.add(tripleQuote("pos2") + ":" + svGenomeVar.getPos2()); - } + Map info) { + if (svGenomeVar.getType() == SVDescription.Type.BND) { + final String contigName2 = + (genomeVersion == GenomeVersion.HG19) + ? svGenomeVar.getChr2Name().replaceFirst("chr", "") + : svGenomeVar.getChr2Name(); - mappings.add( - tripleQuote("backgroundCarriers") - + ":" - + ctx.getCommonInfo().getAttributeAsInt("BACKGROUND_CARRIERS", 0)); - mappings.add( - tripleQuote("affectedCarriers") - + ":" - + ctx.getCommonInfo().getAttributeAsInt("AFFECTED_CARRIERS", 0)); - mappings.add( - tripleQuote("unaffectedCarriers") - + ":" - + ctx.getCommonInfo().getAttributeAsInt("UNAFFECTED_CARRIERS", 0)); + info.put("chr2", contigName2); + info.put("pos2", svGenomeVar.getPos2()); } - return "{" + Joiner.on(",").join(mappings) + "}"; + info.put("backgroundCarriers", ctx.getCommonInfo().getAttributeAsInt("BACKGROUND_CARRIERS", 0)); + info.put("affectedCarriers", ctx.getCommonInfo().getAttributeAsInt("AFFECTED_CARRIERS", 0)); + info.put("unaffectedCarriers", ctx.getCommonInfo().getAttributeAsInt("UNAFFECTED_CARRIERS", 0)); } - private String buildGenotypeValue(VariantContext ctx, int alleleNo) { - - // Add "GT" field. - final List mappings = new ArrayList<>(); - final Comparator c = Comparator.comparing(String::toString); - final List sortedSampleNames = Lists.newArrayList(ctx.getSampleNames()); - sortedSampleNames.sort(c); - for (String sample : sortedSampleNames) { - mappings.add(callerSupport.buildSampleGenotype(ctx, alleleNo, sample).buildStringFragment()); + private Map buildGenotypeValue(VariantContext ctx, int alleleNo) { + final Map result = new TreeMap<>(); + for (String sample : ctx.getSampleNames()) { + result.put(sample, callerSupport.buildSampleGenotype(ctx, alleleNo, sample).toMap()); } - - return "{" + Joiner.on(",").join(mappings) + "}"; + return result; } private static List buildSampleGenotypeValue( diff --git a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/SampleGenotype.java b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/SampleGenotype.java index f65906f..2f7ea56 100644 --- a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/SampleGenotype.java +++ b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/SampleGenotype.java @@ -7,6 +7,8 @@ import com.google.common.collect.ImmutableList; import java.util.ArrayList; import java.util.List; +import java.util.Map; +import java.util.TreeMap; import java.util.stream.Collectors; public final class SampleGenotype { @@ -89,6 +91,42 @@ public String buildStringFragment() { return Joiner.on("").join(tripleQuote(sampleName), ":{", Joiner.on(",").join(attrs), "}"); } + public Map toMap() { + final TreeMap result = new TreeMap<>(); + result.put("gt", genotype); + if (filters != null && !filters.isEmpty()) { + result.put("ft", filters); + } + if (genotypeQuality != null) { + result.put("gq", genotypeQuality); + } + if (pairedEndCoverage != null) { + result.put("pec", pairedEndCoverage); + } + if (pairedEndVariantSupport != null) { + result.put("pev", pairedEndVariantSupport); + } + if (splitReadCoverage != null) { + result.put("src", splitReadCoverage); + } + if (splitReadVariantSupport != null) { + result.put("srv", splitReadVariantSupport); + } + if (averageMappingQuality != null) { + result.put("amq", averageMappingQuality); + } + if (copyNumber != null) { + result.put("cn", copyNumber); + } + if (averageNormalizedCoverage != null) { + result.put("anc", averageNormalizedCoverage); + } + if (pointCount != null) { + result.put("pc", pointCount); + } + return result; + } + public String getSampleName() { return sampleName; } diff --git a/varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordBuilderTest.java b/varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordBuilderTest.java new file mode 100644 index 0000000..666a821 --- /dev/null +++ b/varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordBuilderTest.java @@ -0,0 +1,80 @@ +package com.github.bihealth.varfish_annotator.annotate_svs; + +import java.util.TreeMap; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +public class GenotypeRecordBuilderTest { + + @Test + void testClass() { + GenotypeRecordBuilder builder = new GenotypeRecordBuilder(); + + builder.setRelease("GRCh37"); + builder.setChromosome("chr1"); + builder.setChromosomeNo(1); + builder.setBin(2); + builder.setChromosome2("chr2"); + builder.setChromosomeNo2(3); + builder.setBin2(4); + builder.setPeOrientation("3to5"); + builder.setStart(123); + builder.setEnd(456); + builder.setStartCiLeft(5); + builder.setStartCiRight(6); + builder.setEndCiLeft(7); + builder.setEndCiRight(8); + builder.setCaseId("caseid"); + builder.setSvUuid("svuuid"); + builder.setSetId("setid"); + builder.setCaller("caller"); + builder.setSvType("svtype"); + builder.setSvSubType("svtype:subtype"); + final TreeMap info = new TreeMap(); + info.put("xxx", "yyy"); + builder.setInfo(info); + builder.setNumHomAlt(10); + builder.setNumHomRef(11); + builder.setNumHet(12); + builder.setNumHemiAlt(13); + builder.setNumHemiRef(14); + final TreeMap gt = new TreeMap(); + gt.put("gt", "0/1"); + final TreeMap genotype = new TreeMap(); + genotype.put("sample", gt); + builder.setGenotype(genotype); + + final String expected = + "GenotypeRecordBuilder{release='GRCh37', chromosome='chr1', chromosomeNo=1, bin=2, chromosome2='chr2', chromosomeNo2=3, bin2=4, peOrientation='3to5', start=123, end=456, startCiLeft=5, startCiRight=6, endCiLeft=7, endCiRight=8, caseId='caseid', setId='setid', svUuid='svuuid', caller='caller', svType='svtype', svSubType='svtype:subtype', info={xxx=yyy}, numHomAlt=10, numHomRef=11, numHet=12, numHemiAlt=13, numHemiRef=14, genotype={sample={gt=0/1}}}"; + Assertions.assertEquals(expected, builder.toString()); + + Assertions.assertEquals("GRCh37", builder.getRelease()); + Assertions.assertEquals("chr1", builder.getChromosome()); + Assertions.assertEquals(1, builder.getChromosomeNo()); + Assertions.assertEquals(2, builder.getBin()); + Assertions.assertEquals("chr2", builder.getChromosome2()); + Assertions.assertEquals(3, builder.getChromosomeNo2()); + Assertions.assertEquals(4, builder.getBin2()); + Assertions.assertEquals("3to5", builder.getPeOrientation()); + Assertions.assertEquals(123, builder.getStart()); + Assertions.assertEquals(456, builder.getEnd()); + Assertions.assertEquals(5, builder.getStartCiLeft()); + Assertions.assertEquals(6, builder.getStartCiRight()); + Assertions.assertEquals(7, builder.getEndCiLeft()); + Assertions.assertEquals(8, builder.getEndCiRight()); + Assertions.assertEquals("caseid", builder.getCaseId()); + Assertions.assertEquals("svuuid", builder.getSvUuid()); + Assertions.assertEquals("caller", builder.getCaller()); + Assertions.assertEquals("svtype", builder.getSvType()); + Assertions.assertEquals("svtype:subtype", builder.getSvSubType()); + Assertions.assertEquals("{xxx=yyy}", builder.getInfo().toString()); + Assertions.assertEquals(10, builder.getNumHomAlt()); + Assertions.assertEquals(11, builder.getNumHomRef()); + Assertions.assertEquals(12, builder.getNumHet()); + Assertions.assertEquals(13, builder.getNumHemiAlt()); + Assertions.assertEquals(14, builder.getNumHemiRef()); + Assertions.assertEquals("{sample={gt=0/1}}", builder.getGenotype().toString()); + + final GenotypeRecord record = builder.build(); + } +} diff --git a/varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordTest.java b/varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordTest.java new file mode 100644 index 0000000..a03ce0f --- /dev/null +++ b/varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecordTest.java @@ -0,0 +1,103 @@ +package com.github.bihealth.varfish_annotator.annotate_svs; + +import com.google.common.collect.ImmutableMap; +import java.util.Map; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +public class GenotypeRecordTest { + + @Test + public void testClass() { + final Map info = ImmutableMap.of("xxx", "yyy"); + final Map genotypes = ImmutableMap.of("sample", ImmutableMap.of("gt", "0/1")); + final GenotypeRecord record = + new GenotypeRecord( + "GRCh37", + "chr1", + 1, + 2, + "chr2", + 3, + 4, + "3to5", + 123, + 456, + 5, + 6, + 7, + 8, + "caseid", + "setid", + "svuuid", + "caller", + "svtype", + "svtype:subtype", + info, + 10, + 11, + 12, + 13, + 14, + genotypes); + + Assertions.assertEquals("GRCh37", record.getRelease()); + Assertions.assertEquals("chr1", record.getChromosome()); + Assertions.assertEquals(1, record.getChromosomeNo()); + Assertions.assertEquals(2, record.getBin()); + Assertions.assertEquals("chr2", record.getChromosome2()); + Assertions.assertEquals(3, record.getChromosomeNo2()); + Assertions.assertEquals(4, record.getBin2()); + Assertions.assertEquals("3to5", record.getPeOrientation()); + Assertions.assertEquals(123, record.getStart()); + Assertions.assertEquals(456, record.getEnd()); + Assertions.assertEquals(5, record.getStartCiLeft()); + Assertions.assertEquals(6, record.getStartCiRight()); + Assertions.assertEquals(7, record.getEndCiLeft()); + Assertions.assertEquals(8, record.getEndCiRight()); + Assertions.assertEquals("caseid", record.getCaseId()); + Assertions.assertEquals("svuuid", record.getSvUuid()); + Assertions.assertEquals("caller", record.getCaller()); + Assertions.assertEquals("svtype", record.getSvType()); + Assertions.assertEquals("svtype:subtype", record.getSvSubType()); + Assertions.assertEquals("{xxx=yyy}", record.getInfo().toString()); + Assertions.assertEquals(10, record.getNumHomAlt()); + Assertions.assertEquals(11, record.getNumHomRef()); + Assertions.assertEquals(12, record.getNumHet()); + Assertions.assertEquals(13, record.getNumHemiAlt()); + Assertions.assertEquals(14, record.getNumHemiRef()); + Assertions.assertEquals("{sample={gt=0/1}}", record.getGenotype().toString()); + + Assertions.assertEquals( + "GRCh37\tchr1\t1\t2\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\tcaller\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(false, false)); + Assertions.assertEquals( + "GRCh37\tchr1\t1\t2\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\tcaller\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t10\t11\t12\t13\t14\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(false, true)); + Assertions.assertEquals( + "GRCh37\tchr1\t1\t2\tchr2\t3\t4\t3to5\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\tcaller\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(true, false)); + Assertions.assertEquals( + "GRCh37\tchr1\t1\t2\tchr2\t3\t4\t3to5\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\tcaller\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t10\t11\t12\t13\t14\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(true, true)); + + Assertions.assertTrue(record.equals(record)); + Assertions.assertEquals(record.hashCode(), -1471834423); + } + + @Test + void testGetHeaders() { + Assertions.assertEquals( + "release\tchromosome\tchromosome_no\tbin\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tgenotype", + GenotypeRecord.tsvHeader(false, false)); + Assertions.assertEquals( + "release\tchromosome\tchromosome_no\tbin\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype", + GenotypeRecord.tsvHeader(false, true)); + Assertions.assertEquals( + "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tgenotype", + GenotypeRecord.tsvHeader(true, false)); + Assertions.assertEquals( + "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype", + GenotypeRecord.tsvHeader(true, true)); + } +}