From 1fcf2c840b46c1536e52957933400d2693f01332 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 20 Sep 2022 08:54:18 +0200 Subject: [PATCH] Write out SV callers as array (#81) Closes: #81 Related-Issue: #81 Projected-Results-Impact: none --- CHANGES.md | 5 + .../Case_1_index.delly2.gts.tsv-expected | 4 +- .../annotate_svs/AnnotateSvsVcf.java | 12 +- .../AnnotateDellyVcf37Chr1Test.java | 66 ++--- .../AnnotateDellyVcf37Chr22Test.java | 4 +- .../AnnotateDellyVcf38Chr1Test.java | 24 +- .../grch37-chr1/bwa.delly2.HG00102.bnd.vcf | 135 +--------- .../grch37-chr1/bwa.delly2.HG00102.bnd.vcf.gz | Bin 2121 -> 129 bytes .../bwa.delly2.HG00102.bnd.vcf.gz.tbi | Bin 352 -> 128 bytes .../grch37-chr1/bwa.delly2.HG00102.hemi.vcf | 136 +--------- .../bwa.delly2.HG00102.hemi.vcf.gz | Bin 2201 -> 129 bytes .../bwa.delly2.HG00102.hemi.vcf.gz.tbi | Bin 128 -> 128 bytes .../input/grch37-chr1/bwa.delly2.HG00102.vcf | 138 +--------- .../grch37-chr1/bwa.delly2.HG00102.vcf.gz | Bin 2625 -> 129 bytes .../grch37-chr1/bwa.delly2.HG00102.vcf.gz.tbi | Bin 282 -> 128 bytes .../grch37-chr1/bwa.delly2.NA12878.hemi.vcf | 136 +--------- .../bwa.delly2.NA12878.hemi.vcf.gz | Bin 2322 -> 129 bytes .../bwa.delly2.NA12878.hemi.vcf.gz.tbi | Bin 128 -> 128 bytes .../input/grch37-chr1/bwa.delly2.NA12878.vcf | 138 +--------- .../grch37-chr1/bwa.delly2.NA12878.vcf.gz | Bin 2874 -> 129 bytes .../grch37-chr1/bwa.delly2.NA12878.vcf.gz.tbi | Bin 283 -> 128 bytes .../bwa.gatk_hc.HG00102.asterisk_alleles.vcf | 125 +-------- ...wa.gatk_hc.HG00102.asterisk_alleles.vcf.gz | Bin 4488 -> 129 bytes ...atk_hc.HG00102.asterisk_alleles.vcf.gz.tbi | Bin 119 -> 128 bytes .../grch37-chr1/bwa.gatk_hc.HG00102.hemi.vcf | 127 +-------- .../bwa.gatk_hc.HG00102.hemi.vcf.gz | Bin 5258 -> 129 bytes .../bwa.gatk_hc.HG00102.hemi.vcf.gz.tbi | Bin 126 -> 128 bytes .../input/grch37-chr1/bwa.gatk_hc.HG00102.vcf | 136 +--------- .../grch37-chr1/bwa.gatk_hc.HG00102.vcf.gz | Bin 5782 -> 129 bytes .../bwa.gatk_hc.HG00102.vcf.gz.tbi | Bin 181 -> 128 bytes .../grch37-chr1/bwa.gatk_hc.NA12878.hemi.vcf | 129 +-------- .../bwa.gatk_hc.NA12878.hemi.vcf.gz | Bin 5345 -> 129 bytes .../bwa.gatk_hc.NA12878.hemi.vcf.gz.tbi | Bin 127 -> 128 bytes .../input/grch37-chr1/bwa.gatk_hc.NA12878.vcf | 137 +--------- .../grch37-chr1/bwa.gatk_hc.NA12878.vcf.gz | Bin 5867 -> 129 bytes .../bwa.gatk_hc.NA12878.vcf.gz.tbi | Bin 147 -> 128 bytes .../grch37-chr22/Case_1_index.delly2.vcf.gz | Bin 3373 -> 129 bytes .../Case_1_index.delly2.vcf.gz.tbi | Bin 167 -> 128 bytes .../grch37-chr22/Case_1_index.gatk_hc.vcf.gz | Bin 19137 -> 130 bytes .../Case_1_index.gatk_hc.vcf.gz.tbi | Bin 209 -> 128 bytes .../input/grch38-chr1/bwa.delly2.HG00102.vcf | 247 +---------------- .../grch38-chr1/bwa.delly2.HG00102.vcf.gz | Bin 3463 -> 129 bytes .../grch38-chr1/bwa.delly2.HG00102.vcf.gz.tbi | Bin 287 -> 128 bytes .../input/grch38-chr1/bwa.delly2.NA12878.vcf | 247 +---------------- .../grch38-chr1/bwa.delly2.NA12878.vcf.gz | Bin 3715 -> 129 bytes .../grch38-chr1/bwa.delly2.NA12878.vcf.gz.tbi | Bin 291 -> 128 bytes .../bwa.gatk_hc.HG00102.asterisk_alleles.vcf | 238 +---------------- ...wa.gatk_hc.HG00102.asterisk_alleles.vcf.gz | Bin 9583 -> 129 bytes ...atk_hc.HG00102.asterisk_alleles.vcf.gz.tbi | Bin 109 -> 128 bytes .../input/grch38-chr1/bwa.gatk_hc.HG00102.vcf | 246 +---------------- .../grch38-chr1/bwa.gatk_hc.HG00102.vcf.gz | Bin 10070 -> 130 bytes .../bwa.gatk_hc.HG00102.vcf.gz.tbi | Bin 163 -> 128 bytes .../input/grch38-chr1/bwa.gatk_hc.NA12878.vcf | 248 +----------------- .../grch38-chr1/bwa.gatk_hc.NA12878.vcf.gz | Bin 10311 -> 130 bytes .../bwa.gatk_hc.NA12878.vcf.gz.tbi | Bin 161 -> 128 bytes .../NA-12878WGS_dragen.cnv.gts.tsv | 4 +- .../NA-12878WGS_dragen.sv.gts.tsv | 4 +- .../NA-12878WGS_dragensv_gcnv.gts.tsv | 4 +- ...a.delly2.Case_1_index-N1-DNA1-WGS1.gts.tsv | 4 +- .../bwa.gcnv.NA12878-N1-DNA1-WGS1.gts.tsv | 4 +- .../annotate_svs/GenotypeRecord.java | 104 ++++++-- .../annotate_svs/GenotypeRecordBuilder.java | 17 +- .../annotate_svs/GtRecordBuilder.java | 225 +--------------- .../GenotypeRecordBuilderTest.java | 5 +- .../annotate_svs/GenotypeRecordTest.java | 37 +-- 65 files changed, 243 insertions(+), 2843 deletions(-) diff --git a/CHANGES.md b/CHANGES.md index 3f21f48..6500113 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -2,10 +2,15 @@ ## v0.27 (work in progress) +**IMPORTANT COMPATIBILITY NOTE:** +For annotating SVs, the output of this version is not compatible with `varfish-server` v1.2 (Anthenea) and early versions of the v2 (Bollonaster) development branch. +You can generate compatible files by adding the `--opt-out=chrom2-columns,dbcounts-columns,callers-array` as arguments to `annotate-svs`. + - Writing out proper SV type for Dragen CNV (#76) - Adding support for depth of coverage annotation (#73) - Ensure output files are sorted by chromosomes (#79) - Merge multiple input VCFs in annotate-svs with clustering (#75) +- Write out SV callers as array (#81) ## v0.26 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 1b78b23..3774d2b 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 {"""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}} +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 callers 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 {"""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 58216d4..697b788 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 @@ -500,7 +500,8 @@ private void writeRecords(List chromRecords, Writer writer) thro writer.write( record.toTsv( !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS), - !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS))); + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS), + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CALLERS_ARRAY))); writer.write('\n'); } } @@ -587,7 +588,8 @@ private void checkOptOutFeatures() { ImmutableList.of( GtRecordBuilder.FEATURE_CHROM2_COLUMNS, GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS, - GtRecordBuilder.FEATURE_SUPPRESS_CARRIER_COUNTS); + GtRecordBuilder.FEATURE_SUPPRESS_CARRIER_COUNTS, + GtRecordBuilder.FEATURE_CALLERS_ARRAY); final String features[] = args.getOptOutFeatures().split(","); boolean allGood = true; for (String feature : features) { @@ -651,7 +653,8 @@ private void annotateSvVcf( gtWriter.append( GenotypeRecord.tsvHeader( !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS), - !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS)) + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS), + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CALLERS_ARRAY)) + "\n"); // Write feature-effects header. featureEffectsWriter.append(Joiner.on("\t").join(HEADERS_FEATURE_EFFECTS) + "\n"); @@ -893,7 +896,8 @@ private void annotateVariantContext( gtWriter.append( gtOutRec.toTsv( !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS), - !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS)) + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS), + !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CALLERS_ARRAY)) + "\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_svs/AnnotateDellyVcf37Chr1Test.java b/varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java index 65ade6b..e51aace 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 @@ -157,12 +157,12 @@ void testWithSingleton(boolean gzipOutput) throws IOException { + "GRCh37\thgmd_public\tensembl_r104\n" + "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{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\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" - + "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"; + "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\tcallers\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\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.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" + + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.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\t{\"EMBL.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"; 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( @@ -192,12 +192,12 @@ void testWithTrio(boolean gzipOutput) throws IOException { + "GRCh37\thgmd_public\tensembl_r104\n" + "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{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\"],\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\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" - + "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"; + "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\tcallers\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\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\"],\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n" + + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.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" + + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.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\t{\"EMBL.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"; 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( @@ -254,9 +254,9 @@ void testAnnotateHemiMale() throws Exception { + "GRCh37\thgmd_public\tensembl_r104\n" + "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{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; + "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\tcallers\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\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t0\t1\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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( @@ -285,9 +285,9 @@ void testAnnotateHemiFamily() throws Exception { + "GRCh37\thgmd_public\tensembl_r104\n" + "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{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t1\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\"],\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"gq\"\"\":39,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"; + "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\tcallers\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\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t1\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MAX_PE_AAF\"\"\"],\"\"\"gq\"\"\":127,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t2\t{\"\"\"NA12878\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"ft\"\"\":[\"\"\"MIN_PE_COUNT\"\"\",\"\"\"MIN_SR_AAF\"\"\",\"\"\"MIN_SR_COUNT\"\"\"],\"\"\"gq\"\"\":80,\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"gq\"\"\":24,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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( @@ -319,12 +319,12 @@ void testWithSingletonOptOutChrom2() throws IOException { + "GRCh37\thgmd_public\tensembl_r104\n" + "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{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\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" - + "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"; + "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\tcallers\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\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{\"\"\"affectedCarriers\"\"\":0,\"\"\"backgroundCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t1\t0\t0\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t654\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.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" + + "GRCh37\t1\t1\t780\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.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\t{\"EMBL.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"; 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( @@ -353,12 +353,12 @@ void testWithSingletonOptOutDbCounts() throws IOException { + "GRCh37\thgmd_public\tensembl_r104\n" + "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{}\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\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" - + "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"; + "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\tcallers\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\t{\"EMBL.DELLYv0.8.5\"}\tDEL\tDEL\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t{\"EMBL.DELLYv0.8.5\"}\tDUP\tDUP\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"amq\"\"\":40,\"\"\"anc\"\"\":1.0,\"\"\"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\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.DELLYv0.8.5\"}\tBND\tBND\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21}}\n" + + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.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\t{\"EMBL.DELLYv0.8.5\"}\tBND\tBND\t{}\t{\"\"\"HG00102\"\"\":{\"\"\"gq\"\"\":10000,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"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( @@ -387,9 +387,9 @@ void testWithSingletonBnd() throws IOException { + "GRCh37\thgmd_public\tensembl_r104\n" + "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\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" - + "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"; + "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\tcallers\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\t2486\t2\t2\t2486\t5to3\t249239891\t249239891\t-248\t248\t-248\t248\t.\t.\t00000000-0000-0000-0000-000000000001\t{\"EMBL.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" + + "GRCh37\t2\t2\t585\t1\t1\t585\t3to5\t10265\t10265\t-248\t248\t-248\t248\t.\t.\t00000000-0000-0000-0000-000000000000\t{\"EMBL.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"; 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 0c27332..1867a79 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 @@ -141,8 +141,8 @@ void testWithTrio(boolean gzipOutput) throws IOException { + "GRCh37\tvarfish-annotator\tnull\n" + "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{\"\"\"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"; + "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\tcallers\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\t{\"EMBL.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 72856f6..9f5ace5 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 @@ -116,12 +116,12 @@ void testWithSingleton(boolean gzipOutput) throws IOException { + "GRCh38\tgnomad_genomes\tr2.1.1\n" + "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{\"\"\"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\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" - + "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"; + "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\tcallers\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\t{\"EMBL.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\t{\"EMBL.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\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.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" + + "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.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\t{\"EMBL.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"; 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( @@ -145,12 +145,12 @@ void testWithTrio(boolean gzipOutput) throws IOException { + "GRCh38\tgnomad_genomes\tr2.1.1\n" + "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{\"\"\"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\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" - + "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"; + "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\tcallers\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\t{\"EMBL.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\t{\"EMBL.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\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\t{\"EMBL.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" + + "GRCh38\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\t{\"EMBL.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\t{\"EMBL.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"; 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/resources/input/grch37-chr1/bwa.delly2.HG00102.bnd.vcf b/varfish-annotator-cli/src/test/resources/input/grch37-chr1/bwa.delly2.HG00102.bnd.vcf index 7652c6d..0674280 100644 --- a/varfish-annotator-cli/src/test/resources/input/grch37-chr1/bwa.delly2.HG00102.bnd.vcf +++ b/varfish-annotator-cli/src/test/resources/input/grch37-chr1/bwa.delly2.HG00102.bnd.vcf @@ -1,132 +1,3 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20210512 -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##FILTER= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##reference=/fast/projects/cubit/20.05/static_data/reference/GRCh37/hs37d5/hs37d5.fa -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= 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job_out.796.d/out/tmp_796.vcf.gz job_out.797.d/out/tmp_797.vcf.gz job_out.798.d/out/tmp_798.vcf.gz job_out.799.d/out/tmp_799.vcf.gz job_out.800.d/out/tmp_800.vcf.gz; Date=Mon Oct 11 17:08:07 2021 -##bcftools_viewVersion=1.10.2+htslib-1.10.2-3 -##bcftools_viewCommand=view --header-only /fast/groups/cubi/work/projects/2019-09-17_varfish_demo_data/GRCh38/variant_calling/work/bwa.gatk_hc.HG00102/out/bwa.gatk_hc.HG00102.vcf.gz; Date=Wed Jun 29 10:04:36 2022 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00102 -chr1 129285 rs372768449 G A 46.28 . AC=2;AF=1;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=20;QD=15.43;SOR=2.833 GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 -chr1 185194 . G C 20.8 . AC=1;AF=0.5;AN=2;BaseQRankSum=-0.771;ClippingRankSum=0;DP=12;ExcessHet=3.0103;FS=2.932;MLEAC=1;MLEAF=0.5;MQ=23.3;MQRankSum=0.23;QD=1.73;ReadPosRankSum=1.139;SOR=1.828 GT:AD:DP:GQ:PL 0/1:9,3:12:49:49,0,199 -chr1 185428 . A G 64.77 . AC=1;AF=0.5;AN=2;BaseQRankSum=-0.135;ClippingRankSum=0;DP=8;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=23.15;MQRankSum=0.272;QD=8.1;ReadPosRankSum=1.465;SOR=0.368 GT:AD:DP:GQ:PL 0/1:5,3:8:93:93,0,114 -chr1 185451 . A G 13.95 . AC=1;AF=0.5;AN=2;BaseQRankSum=0.524;ClippingRankSum=0;DP=5;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=27.96;MQRankSum=-0.524;QD=2.79;ReadPosRankSum=0.253;SOR=1.609 GT:AD:DP:GQ:PL 0/1:3,2:5:42:42,0,145 -chr1 186536 . C T 64.77 . AC=1;AF=0.5;AN=2;BaseQRankSum=0.253;ClippingRankSum=0;DP=6;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=23.03;MQRankSum=0;QD=10.79;ReadPosRankSum=-1.282;SOR=1.609 GT:AD:DP:GQ:PL 0/1:2,4:6:37:93,0,37 -chr1 187485 . G A 93.77 . AC=1;AF=0.5;AN=2;BaseQRankSum=-0.644;ClippingRankSum=0;DP=24;ExcessHet=3.0103;FS=5.351;MLEAC=1;MLEAF=0.5;MQ=25.54;MQRankSum=0.597;QD=3.91;ReadPosRankSum=1.188;SOR=0.037 GT:AD:DP:GQ:PL 0/1:17,7:24:99:122,0,425 -chr1 809990 rs146246821 TA T 17.8 . AC=1;AF=0.5;AN=2;BaseQRankSum=0.88;ClippingRankSum=0;DB;DP=19;ExcessHet=3.0103;FS=8.016;MLEAC=1;MLEAF=0.5;MQ=38.91;MQRankSum=-1.808;QD=0.94;ReadPosRankSum=-1.063;SOR=0.008 GT:AD:DP:GQ:PL 0/1:16,3:19:55:55,0,541 -chr1 873251 rs11240779 G A 531.77 . AC=2;AF=1;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=59.42;QD=34.24;SOR=3.767 GT:AD:DP:GQ:PL 1/1:0,13:13:39:560,39,0 -chr1 930165 . G A 2872.77 . 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AC=4;AF=1;AN=4;DB;DP=4;ExcessHet=3.0103;FS=0;MLEAC=4;MLEAF=1;MQ=43.15;QD=30.41;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 1/1:0,1:1:3:25,3,0 ./.:.:.:.:. -chr1 69270 rs201219564 A G 63.42 . AC=2;AF=1;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=25;QD=21.14;SOR=2.833 GT:AD:DP:GQ:PL ./.:.:.:.:. ./.:.:.:.:. 1/1:0,3:3:9:89,9,0 -chr1 69511 rs2691305 A G 620.14 . AC=2;AF=0.5;AN=4;BaseQRankSum=1.573;ClippingRankSum=0;DB;DP=25;ExcessHet=0.7918;FS=0;MLEAC=3;MLEAF=0.75;MQ=36.64;MQRankSum=0.984;QD=31.01;ReadPosRankSum=-1.329;SOR=0.223 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,25 ./.:.:.:.:. 1/1:0,20:20:60:650,60,0 -chr1 129285 rs372768449 G A 149.32 . AC=4;AF=1;AN=4;DB;DP=7;ExcessHet=3.0103;FS=0;MLEAC=4;MLEAF=1;MQ=20.3;QD=21.33;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 1/1:0,4:4:12:101,12,0 ./.:.:.:.:. -chr1 186536 . C T 42.89 . AC=2;AF=0.5;AN=4;BaseQRankSum=-1.486;ClippingRankSum=0;DP=15;ExcessHet=4.7712;FS=6.166;MLEAC=2;MLEAF=0.5;MQ=23.78;MQRankSum=-2.18;QD=5.36;ReadPosRankSum=0.682;SOR=0.069 GT:AD:DP:GQ:PL 0/1:4,4:8:64:64,0,87 0/1:6,1:7:6:6,0,153 ./.:.:.:.:. -chr1 186893 . T A 21.93 . AC=1;AF=0.5;AN=2;BaseQRankSum=-0.21;ClippingRankSum=0;DP=10;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=37.24;MQRankSum=-0.015;QD=2.44;ReadPosRankSum=0.531;SOR=1.179 GT:AD:DP:GQ:PL ./.:.:.:.:. 0/1:6,3:9:48:48,0,143 ./.:.:.:.:. -chr1 187019 . G A 148.57 . AC=3;AF=0.75;AN=4;BaseQRankSum=1.331;ClippingRankSum=0;DP=10;ExcessHet=3.0103;FS=5.229;MLEAC=3;MLEAF=0.75;MQ=36.17;MQRankSum=-1.687;QD=14.86;ReadPosRankSum=-0.063;SOR=3.383 GT:AD:DP:GQ:PL 1/1:0,3:3:9:100,9,0 0/1:3,4:7:56:77,0,56 ./.:.:.:.:. -chr1 187102 . C G 101.57 . AC=1;AF=0.25;AN=4;BaseQRankSum=-0.989;ClippingRankSum=0;DP=21;ExcessHet=3.9794;FS=1.949;MLEAC=2;MLEAF=0.5;MQ=42.74;MQRankSum=1.626;QD=8.46;ReadPosRankSum=-0.214;SOR=0.28 GT:AD:DP:GQ:PL ./.:.:.:.:. 0/1:6,6:12:99:127,0,166 ./.:.:.:.:. -chr1 930165 . G A 2159.89 . AC=3;AF=0.75;AN=4;BaseQRankSum=1.3;ClippingRankSum=0;DP=103;ExcessHet=3.0103;FS=8.266;MLEAC=3;MLEAF=0.75;MQ=31.03;MQRankSum=-2.307;QD=21.18;ReadPosRankSum=-0.409;SOR=1.79 GT:AD:DP:GQ:PL 1/1:1,37:38:89:1194,89,0 0/1:21,43:64:99:995,0,371 ./.:.:.:.:. -chr1 930317 . A G 65.89 . 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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:f0e4bce757595ed5776efa23fff304ecc46dc22e76287bbe2faf05fad656f814 -size 189559 +oid sha256:d5875cb55359521ebe235692cd35e5269eebb6b2b1c270c91aea9032c5ecfc99 +size 191832 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 6c61d49..1f1eb74 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 sha256:5e80badaf197f5a64219a90a7bcc2f8f2a7d4cd98d0ba00a4818cb948d1b15ac -size 2841266 +oid sha256:c00b10793758b8ee8711d4006a93e2234dd2ae82cb2f4e11c5aaa4f84612d00c +size 2875011 diff --git a/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragensv_gcnv.gts.tsv b/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragensv_gcnv.gts.tsv index 2abfbe8..e842eaa 100644 --- a/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragensv_gcnv.gts.tsv +++ b/varfish-annotator-cli/src/test/resources/input/real-world-37/NA-12878WGS_dragensv_gcnv.gts.tsv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:1f0f353a5a6d2d9217da1892a820128c03af37aa44d0306f5b3dea35d30f65c5 -size 2957312 +oid sha256:320f5d0e04eded1d12196756aecaae34af34bf7b8ba0d17ace86e2c1ff17fba0 +size 2990080 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 2f1145b..6502f0d 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 sha256:933fce365a00041be94817ef191c08ad1cbc4b5d130aeadcdc8eb54b14b905b6 -size 19498392 +oid sha256:47578a2f0e39b19b26112e2997c92cfd05e8d90f52f49587fcc02da80b1bacd7 +size 19624825 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 21307b1..9177d62 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:af3fca47e687a79fdfced8fff1a1c1854580f7b4f1f76569b765571fd8704d70 -size 155415 +oid sha256:fa612adf95aa30819186cf0fcc564a189ca6d1a939406470712f706dee8cd805 +size 157592 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 index e6eab2f..85bd157 100644 --- 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 @@ -8,6 +8,10 @@ import com.google.common.collect.ImmutableList; import com.google.common.collect.ImmutableMap; import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.List; +import java.util.Map; import org.json.JSONArray; import org.json.JSONObject; @@ -19,7 +23,7 @@ public class GenotypeRecord { 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 = + private static final ImmutableList HEADERS_GT_PART_3_1 = ImmutableList.of( "start", "end", @@ -29,11 +33,10 @@ public class GenotypeRecord { "end_ci_right", "case_id", "set_id", - "sv_uuid", - "caller", - "sv_type", - "sv_sub_type", - "info"); + "sv_uuid"); + + private static final ImmutableList HEADERS_GT_PART_3_2 = + ImmutableList.of("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"); @@ -58,6 +61,7 @@ public class GenotypeRecord { private final String setId; private final String svUuid; private final String caller; + private final ImmutableList callers; private final String svType; private final String svSubType; private final ImmutableMap info; @@ -88,6 +92,7 @@ public GenotypeRecord( String setId, String svUuid, String caller, + Collection callers, String svType, String svSubType, Map info, @@ -115,6 +120,7 @@ public GenotypeRecord( this.setId = setId; this.svUuid = svUuid; this.caller = caller; + this.callers = ImmutableList.copyOf(callers); this.svType = svType; this.svSubType = svSubType; this.info = ImmutableMap.copyOf(info); @@ -126,14 +132,21 @@ public GenotypeRecord( this.genotype = ImmutableMap.copyOf(genotype); } - public static String tsvHeader(boolean showChrom2Columns, boolean showDbCountColumns) { + public static String tsvHeader( + boolean showChrom2Columns, boolean showDbCountColumns, boolean showCallersArrayColumn) { // (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); + headers.addAll(HEADERS_GT_PART_3_1); + if (showCallersArrayColumn) { + headers.add("callers"); + } else { + headers.add("caller"); + } + headers.addAll(HEADERS_GT_PART_3_2); if (showDbCountColumns) { headers.addAll(HEADERS_GT_PART_4); } @@ -201,6 +214,9 @@ public static GenotypeRecord fromTsv(List values, List headers) case "caller": builder.setCaller(value); break; + case "callers": + builder.setCallers(parseArray(value)); + break; case "sv_type": builder.setSvType(value); break; @@ -232,9 +248,37 @@ public static GenotypeRecord fromTsv(List values, List headers) throw new RuntimeException("Unknown header: " + header); } } + + // Handle the case that either case/cases is empty and the other is not. + if ((builder.getCaller() == null || ".".equals(builder.getCaller())) + && !builder.getCallers().isEmpty()) { + builder.setCaller(Joiner.on(";").join(builder.getCallers())); + } else if ((builder.getCaller() != null && !".".equals(builder.getCaller())) + && builder.getCallers().isEmpty()) { + builder.setCallers(Arrays.asList(builder.getCaller().split(";"))); + } + return builder.build(); } + private static List parseArray(String value) { + if (!value.startsWith("{") || !value.endsWith("}")) { + throw new RuntimeException("Could not parse postgres array from: " + value); + } else { + final List result = new ArrayList<>(); + final String[] split = value.substring(1, value.length() - 1).split(","); + for (int i = 0; i < split.length; i++) { + final String s = split[i]; + if (s.startsWith("\"")) { + result.add(s.substring(1, s.length() - 1)); + } else { + result.add(s); + } + } + return result; + } + } + private static Map parseJsonObjectValue(String value) { if (!value.startsWith("{") || !value.endsWith("}")) { throw new RuntimeException("Not a valid JSON object: " + value); @@ -261,25 +305,34 @@ private static Map jsonObjectToMap(JSONObject jsonObject) { return result; } - public String toTsv(boolean showChrom2Columns, boolean showDbCountColumns) { + public String toTsv( + boolean showChrom2Columns, boolean showDbCountColumns, boolean showCallersArrayColumn) { 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); + start, end, startCiLeft, startCiRight, endCiLeft, endCiRight, caseId, setId, svUuid); + if (showCallersArrayColumn) { + final ImmutableList.Builder innerBuilder = ImmutableList.builder(); + innerBuilder.add("{"); + boolean first = true; + for (String caller : callers) { + if (!first) { + innerBuilder.add(","); + } + innerBuilder.add("\""); + innerBuilder.add(caller); + innerBuilder.add("\""); + first = false; + } + innerBuilder.add("}"); + builder.add(Joiner.on("").join(innerBuilder.build())); + } else { + builder.add(caller); + } + builder.add(svType, svSubType); builder.add(convert(info)); if (showDbCountColumns) { builder.add(numHomAlt, numHomRef, numHet, numHemiAlt, numHemiRef); @@ -402,6 +455,10 @@ public String getCaller() { return caller; } + public ImmutableList getCallers() { + return callers; + } + public String getSvType() { return svType; } @@ -485,6 +542,9 @@ public String toString() { + ", caller='" + caller + '\'' + + ", callers='" + + callers + + '\'' + ", svType='" + svType + '\'' @@ -536,6 +596,7 @@ && getEndCiRight() == that.getEndCiRight() && Objects.equal(getSetId(), that.getSetId()) && Objects.equal(getSvUuid(), that.getSvUuid()) && Objects.equal(getCaller(), that.getCaller()) + && Objects.equal(getCallers(), that.getCallers()) && Objects.equal(getSvType(), that.getSvType()) && Objects.equal(getSvSubType(), that.getSvSubType()) && Objects.equal(getInfo(), that.getInfo()) @@ -563,6 +624,7 @@ public int hashCode() { getSetId(), getSvUuid(), getCaller(), + callers, getSvType(), getSvSubType(), getInfo(), 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 index e34cd92..b3b1b57 100644 --- 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 @@ -1,7 +1,6 @@ package com.github.bihealth.varfish_annotator.annotate_svs; -import java.util.Map; -import java.util.TreeMap; +import java.util.*; /** Helper for building {@code GenotypeRecord} objects. */ public class GenotypeRecordBuilder { @@ -23,6 +22,7 @@ public class GenotypeRecordBuilder { private String setId; private String svUuid; private String caller; + private List callers = new ArrayList<>(); private String svType; private String svSubType; private Map info = new TreeMap(); @@ -85,6 +85,7 @@ public GenotypeRecord build() { setId, svUuid, caller, + callers, svType, svSubType, info, @@ -236,10 +237,19 @@ public String getCaller() { return caller; } + public List getCallers() { + return callers; + } + public void setCaller(String caller) { this.caller = caller; } + public void setCallers(Collection callers) { + this.callers = new ArrayList<>(); + this.callers.addAll(callers); + } + public String getSvType() { return svType; } @@ -361,6 +371,9 @@ public String toString() { + ", caller='" + caller + '\'' + + ", callers='" + + callers + + '\'' + ", svType='" + svType + '\'' 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 0fcb8a6..b5c38eb 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 @@ -1,21 +1,14 @@ package com.github.bihealth.varfish_annotator.annotate_svs; -import static com.github.bihealth.varfish_annotator.utils.StringUtils.tripleQuote; - import com.github.bihealth.varfish_annotator.data.GenomeVersion; import com.github.bihealth.varfish_annotator.utils.GenotypeCounts; import com.github.bihealth.varfish_annotator.utils.UcscBinning; -import com.google.common.base.Joiner; import com.google.common.collect.ImmutableList; -import com.google.common.primitives.Ints; import de.charite.compbio.jannovar.pedigree.Pedigree; import de.charite.compbio.jannovar.reference.SVDescription; import de.charite.compbio.jannovar.reference.SVGenomeVariant; -import htsjdk.variant.variantcontext.Allele; -import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import java.util.*; -import java.util.stream.Collectors; /** Helper class for building record for {@code .gts.tsv} file. */ public class GtRecordBuilder { @@ -23,6 +16,7 @@ public class GtRecordBuilder { public static final String FEATURE_CHROM2_COLUMNS = "chrom2-columns"; public static final String FEATURE_DBCOUNTS_COLUMNS = "dbcounts-columns"; public static final String FEATURE_SUPPRESS_CARRIER_COUNTS = "suppress-carriers-in-info"; + public static final String FEATURE_CALLERS_ARRAY = "callers-array"; private final String release; private final String defaultSvMethod; @@ -99,6 +93,9 @@ public GenotypeRecord buildRecord( svMethod = defaultSvMethod == null ? "." : defaultSvMethod; } builder.setCaller(svMethod); + if (!".".equals(svMethod)) { + builder.setCallers(ImmutableList.of(svMethod)); + } builder.setSvType(svGenomeVar.getType().toString()); builder.setSvSubType(svGenomeVar.getType().toString()); @@ -147,102 +144,6 @@ private String getPeOrientation(VariantContext ctx, SVGenomeVariant svGenomeVar, } } - public List buildRecordOld( - UUID variantId, - SVGenomeVariant svGenomeVar, - VariantContext ctx, - GenomeVersion genomeVersion, - int alleleNo) { - String svMethod = ctx.getCommonInfo().getAttributeAsString("SVMETHOD", null); - if (svMethod == null) { - svMethod = defaultSvMethod == null ? "." : defaultSvMethod; - } - - final int bin; - final int bin2; - final int pos2; - if (svGenomeVar.getType() == SVDescription.Type.BND) { - pos2 = svGenomeVar.getPos() + 1; - bin = UcscBinning.getContainingBin(svGenomeVar.getPos(), svGenomeVar.getPos() + 1); - bin2 = UcscBinning.getContainingBin(pos2, pos2 + 1); - } else { - pos2 = svGenomeVar.getPos2(); - bin = UcscBinning.getContainingBin(svGenomeVar.getPos(), pos2); - bin2 = bin; - } - - final String contigName = - (genomeVersion == GenomeVersion.HG19) - ? svGenomeVar.getChrName().replaceFirst("chr", "") - : svGenomeVar.getChrName(); - final String contigName2 = - (genomeVersion == GenomeVersion.HG19) - ? svGenomeVar.getChr2Name().replaceFirst("chr", "") - : svGenomeVar.getChr2Name(); - - final ImmutableList.Builder result = ImmutableList.builder(); - // part 1 - result.add(release, contigName, svGenomeVar.getChr(), bin); - // optional part 2 - if (!optOutFeatures.contains(FEATURE_CHROM2_COLUMNS)) { - final String peOrientation; - if (svGenomeVar.getType() == SVDescription.Type.INV) { - peOrientation = "3to3"; - } else if (svGenomeVar.getType() == SVDescription.Type.DUP) { - peOrientation = "5to3"; - } else if (svGenomeVar.getType() == SVDescription.Type.DEL) { - peOrientation = "3to5"; - } else if (svGenomeVar.getType() == SVDescription.Type.BND) { - final String altBases = ctx.getAlternateAllele(alleleNo - 1).getDisplayString(); - if (altBases.startsWith("[")) { - peOrientation = "3to5"; - } else if (altBases.startsWith("]")) { - peOrientation = "5to3"; - } else if (altBases.endsWith("[")) { - peOrientation = "3to5"; - } else if (altBases.endsWith("]")) { - peOrientation = "3to3"; - } else { - peOrientation = "."; - } - } else { - peOrientation = "."; - } - result.add(contigName2, svGenomeVar.getChr2(), bin2, peOrientation); - } - // part 3 - result.add( - svGenomeVar.getPos() + 1, - pos2, - svGenomeVar.getPosCILowerBound(), - svGenomeVar.getPosCIUpperBound(), - svGenomeVar.getPos2CILowerBound(), - svGenomeVar.getPos2CIUpperBound(), - caseId, - setId, - variantId.toString(), - svMethod, - // TODO: improve type and sub type annotation! - svGenomeVar.getType(), - svGenomeVar.getType(), - ""); // buildInfoValue(ctx, genomeVersion, svGenomeVar, optOutFeatures)); - // optional part 4 - if (!optOutFeatures.contains(FEATURE_DBCOUNTS_COLUMNS)) { - final GenotypeCounts gtCounts = - GenotypeCounts.buildGenotypeCounts(ctx, alleleNo, pedigree, release); - result.add( - String.valueOf(gtCounts.numHomAlt), - String.valueOf(gtCounts.numHomRef), - String.valueOf(gtCounts.numHet), - String.valueOf(gtCounts.numHemiAlt), - String.valueOf(gtCounts.numHemiRef)); - } - // part 5 - // result.add(buildGenotypeValue(ctx, alleleNo)); - - return result.build(); - } - private static void augmentInfoValue( VariantContext ctx, GenomeVersion genomeVersion, @@ -270,122 +171,4 @@ private Map buildGenotypeValue(VariantContext ctx, int alleleNo) } return result; } - - private static List buildSampleGenotypeValue( - VariantContext ctx, int alleleNo, String sample) { - final ArrayList attrs = new ArrayList<>(); - - final Genotype genotype = ctx.getGenotype(sample); - final Map gts = new TreeMap<>(); - final List gtList = new ArrayList<>(); - for (Allele allele : genotype.getAlleles()) { - if (allele.isNoCall()) { - gtList.add("."); - } else if (ctx.getAlleleIndex(allele) == alleleNo) { - gtList.add("1"); - } else { - gtList.add("0"); - } - } - if (genotype.isPhased()) { - gts.put(sample, Joiner.on("|").join(gtList)); - } else { - gtList.sort(Comparator.naturalOrder()); - gts.put(sample, Joiner.on("/").join(gtList)); - } - attrs.add(Joiner.on("").join(tripleQuote("gt"), ":", tripleQuote(gts.get(sample)))); - - // FT -- genotype filters - if (genotype.hasExtendedAttribute("FT") - && genotype.getFilters() != null - && !genotype.getFilters().equals("")) { - final List fts = - Arrays.stream(genotype.getFilters().split(",")) - .map(s -> tripleQuote(s)) - .collect(Collectors.toList()); - attrs.add(Joiner.on("").join(tripleQuote("ft"), ":[", Joiner.on(",").join(fts), "]")); - } - - // GQ -- genotype quality - if (genotype.hasGQ()) { - attrs.add(Joiner.on("").join(tripleQuote("gq"), ":", genotype.getGQ())); - } - - // Additional integer attributes, currently Delly only. - boolean looksLikeDelly = ctx.getAttributeAsString("SVMETHOD", "").contains("DELLY"); - boolean looksLikeXHMM = ctx.getAttributeAsString("SVMETHOD", "").contains("XHMM"); - boolean looksLikeGcnv = ctx.getAttributeAsString("SVMETHOD", "").contains("gcnvkernel"); - if (looksLikeDelly) { - // * DR -- reference pairs - // * DV -- variant pairs - // * RR -- reference junction - // * RV -- variant junction - final int dr = Integer.parseInt(genotype.getExtendedAttribute("DR", "0").toString()); - final int dv = Integer.parseInt(genotype.getExtendedAttribute("DV", "0").toString()); - final int rr = Integer.parseInt(genotype.getExtendedAttribute("RR", "0").toString()); - final int rv = Integer.parseInt(genotype.getExtendedAttribute("RV", "0").toString()); - - // Attributes to write out. - // - // * pec - paired end coverage - // * pev - paired end variant support - // * src - split read coverage - // * srv - split read end variant support - attrs.add(Joiner.on("").join(tripleQuote("pec"), ":", String.valueOf(dr + dv))); - attrs.add(Joiner.on("").join(tripleQuote("pev"), ":", String.valueOf(dv))); - attrs.add(Joiner.on("").join(tripleQuote("src"), ":", String.valueOf(rr + rv))); - attrs.add(Joiner.on("").join(tripleQuote("srv"), ":", String.valueOf(rv))); - } else if (looksLikeXHMM) { - // * DQ -- diploid quality - // * NDQ -- non-diploid quality - // * RD -- mean normalized read depth over region - // * PL -- genotype likelihoods, for [diploid, deletion, duplication] - final float dq = Float.parseFloat(genotype.getExtendedAttribute("DQ", "0.0").toString()); - final float ndq = Float.parseFloat(genotype.getExtendedAttribute("NDQ", "0.0").toString()); - final float rd = Float.parseFloat(genotype.getExtendedAttribute("RD", "0.0").toString()); - final int pl[] = genotype.getPL(); - - // Attributes to write out. - // - // * dq -- diploid quality - // * ndq -- non-diploid quality - // * rd -- mean normalized read depth over region - // * pl -- genotype likelihoods, for [diploid, deletion, duplication] - attrs.add(Joiner.on("").join(tripleQuote("dq"), ":", String.valueOf(dq))); - attrs.add(Joiner.on("").join(tripleQuote("ndq"), ":", String.valueOf(ndq))); - attrs.add(Joiner.on("").join(tripleQuote("rd"), ":", String.valueOf(rd))); - attrs.add( - Joiner.on("").join(tripleQuote("pl"), ":[", Joiner.on(',').join(Ints.asList(pl)), "]")); - } else if (looksLikeGcnv) { - // * CN -- copy number - // * NP -- number of points in segment - // * QA -- phred-scaled quality of all points agreeing - // * QS -- phred-scaled quality of at least one point agreeing - // * QSS -- phred-scaled quality of start breakpoint - // * QSE -- phred-scaled quality of end breakpoint - final int cn = Integer.parseInt(genotype.getExtendedAttribute("CN", "0").toString()); - final int np = Integer.parseInt(genotype.getExtendedAttribute("NP", "0").toString()); - final int qa = Integer.parseInt(genotype.getExtendedAttribute("QA", "0").toString()); - final int qs = Integer.parseInt(genotype.getExtendedAttribute("QS", "0").toString()); - final int qss = Integer.parseInt(genotype.getExtendedAttribute("QSS", "0").toString()); - final int qse = Integer.parseInt(genotype.getExtendedAttribute("QSE", "0").toString()); - - // Attributes to write out. - // - // * cn -- copy number - // * np -- number of points in segment - // * qa -- phred-scaled quality of all points agreeing - // * qs -- phred-scaled quality of at least one point agreeing - // * qss -- phred-scaled quality of start breakpoint - // * qse -- phred-scaled quality of end breakpoint - attrs.add(Joiner.on("").join(tripleQuote("cn"), ":", String.valueOf(cn))); - attrs.add(Joiner.on("").join(tripleQuote("np"), ":", String.valueOf(np))); - attrs.add(Joiner.on("").join(tripleQuote("qa"), ":", String.valueOf(qa))); - attrs.add(Joiner.on("").join(tripleQuote("qs"), ":", String.valueOf(qs))); - attrs.add(Joiner.on("").join(tripleQuote("qss"), ":", String.valueOf(qss))); - attrs.add(Joiner.on("").join(tripleQuote("qse"), ":", String.valueOf(qse))); - } - - return attrs; - } } 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 index 666a821..ea4da3c 100644 --- 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 @@ -1,5 +1,6 @@ package com.github.bihealth.varfish_annotator.annotate_svs; +import com.google.common.collect.ImmutableList; import java.util.TreeMap; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; @@ -28,6 +29,7 @@ void testClass() { builder.setSvUuid("svuuid"); builder.setSetId("setid"); builder.setCaller("caller"); + builder.setCallers(ImmutableList.of("caller")); builder.setSvType("svtype"); builder.setSvSubType("svtype:subtype"); final TreeMap info = new TreeMap(); @@ -45,7 +47,7 @@ void testClass() { 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}}}"; + "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', callers='[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()); @@ -65,6 +67,7 @@ void testClass() { Assertions.assertEquals("caseid", builder.getCaseId()); Assertions.assertEquals("svuuid", builder.getSvUuid()); Assertions.assertEquals("caller", builder.getCaller()); + Assertions.assertEquals("[caller]", builder.getCallers().toString()); Assertions.assertEquals("svtype", builder.getSvType()); Assertions.assertEquals("svtype:subtype", builder.getSvSubType()); Assertions.assertEquals("{xxx=yyy}", builder.getInfo().toString()); 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 index a03ce0f..fe29e18 100644 --- 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 @@ -1,5 +1,6 @@ package com.github.bihealth.varfish_annotator.annotate_svs; +import com.google.common.collect.ImmutableList; import com.google.common.collect.ImmutableMap; import java.util.Map; import org.junit.jupiter.api.Assertions; @@ -31,6 +32,7 @@ public void testClass() { "setid", "svuuid", "caller", + ImmutableList.of("caller"), "svtype", "svtype:subtype", info, @@ -58,6 +60,7 @@ public void testClass() { Assertions.assertEquals("caseid", record.getCaseId()); Assertions.assertEquals("svuuid", record.getSvUuid()); Assertions.assertEquals("caller", record.getCaller()); + Assertions.assertEquals("[caller]", record.getCallers().toString()); Assertions.assertEquals("svtype", record.getSvType()); Assertions.assertEquals("svtype:subtype", record.getSvSubType()); Assertions.assertEquals("{xxx=yyy}", record.getInfo().toString()); @@ -69,35 +72,35 @@ public void testClass() { 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)); + "GRCh37\tchr1\t1\t2\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\t{\"caller\"}\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(false, false, true)); 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)); + "GRCh37\tchr1\t1\t2\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\t{\"caller\"}\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t10\t11\t12\t13\t14\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(false, true, 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)); + "GRCh37\tchr1\t1\t2\tchr2\t3\t4\t3to5\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\t{\"caller\"}\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(true, 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\"\"\"}\t10\t11\t12\t13\t14\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", - record.toTsv(true, true)); + "GRCh37\tchr1\t1\t2\tchr2\t3\t4\t3to5\t123\t456\t5\t6\t7\t8\tcaseid\tsetid\tsvuuid\t{\"caller\"}\tsvtype\tsvtype:subtype\t{\"\"\"xxx\"\"\":\"\"\"yyy\"\"\"}\t10\t11\t12\t13\t14\t{\"\"\"sample\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\"}}", + record.toTsv(true, true, true)); Assertions.assertTrue(record.equals(record)); - Assertions.assertEquals(record.hashCode(), -1471834423); + Assertions.assertEquals(record.hashCode(), 1311944769); } @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)); + "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\tcallers\tsv_type\tsv_sub_type\tinfo\tgenotype", + GenotypeRecord.tsvHeader(false, false, true)); 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)); + "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\tcallers\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, 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)); + "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\tcallers\tsv_type\tsv_sub_type\tinfo\tgenotype", + GenotypeRecord.tsvHeader(true, 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\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype", - GenotypeRecord.tsvHeader(true, true)); + "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\tcallers\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, true)); } }