Adding explicit support for SV/CNV calling tools (#68)

Closes: #68 Closes: #60 Related-Issue: #68 Projected-Results-Impact: none
varfish-org · Sep 14, 2022 · 23dfad3 · 23dfad3
1 parent 753aea5
commit 23dfad3
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diff --git a/README.md b/README.md
@@ -43,9 +43,24 @@ The following fields are considered:
 
 ### Structural Variants / Copy Number Variants
 
-Note that if the `INFO/SVMETHOD` field is missing then you should define `--default-sv-method` as you would otherwise get a problem downstream.
+**Supported Callers and Caller Annotation**
+
+The following variant callers are explicitely supported.
+In the other cases, VarFish annotator will fall back to a "generic" import where only the per-sample fields `GT`, `FT`, and `GQ` are interpreted.
+
+- Delly 2 (SVs)
+- Dragen CNV caller
+- Dragen SV caller
+- Manta
+- GATK gCNV
+- XHMM (deprecated)
+
+VarFish Annotator will look at the field `INFO/SVMETHOD` to annotate calls with the caller where the call originated from.
+If this field is empty then you should define `--default-sv-method` so you get appropriately labeled output.
 If you have any problem with your data then please tell us by opening a GitHub issue.
 
+**Interpretation of top-level and INFO VCF fields**
+
 The following fields are considered:
 
 - `CHROM`
@@ -70,28 +85,32 @@ The following fields are considered:
   Confidence interval around the end point of the SV.
 - `INFO/SVMETHOD`
   The name of the caller that was used.
-- `FORMAT` and per `SAMPLE`
-  - Common
-    - `GT` Genotype
-    - `FT` Per-genotype filter values
-    - `GQ` Phred-scaled genotype quality
-  - For Delly2
-    - `DR` Reference pairs
-    - `DV` Variant pairs
-    - `RR` Reference junction count
-    - `RV` Variant junction count
-  - For XHMM
-    - `DQ` Diploid Quality
-    - `NDQ` Non-diploid Quality
-    - `RD` Mean normalized read depth over region
-    - `PL` Genotype likelihoods for [diploid, deletion, duplication]
-  - For GATK gCNV
-     - `CN` Copy number
-     - `NP` Number of points in segment
-     - `QA` Phred-scale quality of all points agreeing
-     - `QS` Phred-scaled quality of least one point agreeing
-     - `QSS` Phred-scaled quality of start breakpoint
-     - `QSE` Phred-scaled quality of end breakpoint
+
+**Interpretation of `FORMAT` and per sample fields**
+
+- Common
+  - `GT` Genotype, written as `gt`
+  - `FT` Per-genotype filter values, written as `ft`
+  - `GQ` Phred-scaled genotype quality, written as `gq`
+- Delly2
+  - `DR` Reference pairs, written as `pec = DR + DV`
+  - `DV` Variant pairs, written as `pev`
+  - `RR` Reference junction count, written as `src = RR + RV`
+  - `RV` Variant junction count, written as `srv`
+  - `RDCN` Copy number estimate, written as `cn`
+- Dragen CNV
+  - `SM` Average normalized overage, written as `anc`
+  - `BC` Bucket count, written as point count `pc`
+  - `PE` Discordante read count at start/end, written as `pev = PE[0] + PE[1]`
+- Dragen SV
+  - `PR` Paired read of reference and variant, written as `pec = PR[0] + PR[1]` and `pev = PR[1]`
+  - `SR` Paired read of reference and variant, written as `src = SR[0] + SR[1]` and `srv = SR[1]`
+- For GATK gCNV
+  - `CN` Integer copy number, written as `cn`
+  - `NP` Number of points in segment, written as `np`
+- Manta (equivalent to Dragen SV)
+- For XHMM
+    - `RD` Average normalized coveage, written as `an`
 
 ## Example
 

diff --git a/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected b/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected
@@ -1,2 +1,2 @@
 release	chromosome	chromosome_no	bin	chromosome2	chromosome_no2	bin2	pe_orientation	start	end	start_ci_left	start_ci_right	end_ci_left	end_ci_right	case_id	set_id	sv_uuid	caller	sv_type	sv_sub_type	info	num_hom_alt	num_hom_ref	num_het	num_hemi_alt	num_hemi_ref	genotype
-GRCh37	22	22	89	22	22	89	3to5	17400000	17700000	-29	29	-29	29	.	.	UUID	EMBL.DELLYv1.1.3	DEL	DEL	{"""backgroundCarriers""":0,"""affectedCarriers""":0,"""unaffectedCarriers""":0}	0	2	1	0	0	{"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4,"""gt""":"""0/0""","""gq""":35,"""pec""":0,"""pev""":0,"""src""":29,"""srv""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4,"""gt""":"""0/0""","""gq""":35,"""pec""":0,"""pev""":0,"""src""":29,"""srv""":2,"""gt""":"""0/0""","""gq""":67,"""pec""":0,"""pev""":0,"""src""":32,"""srv""":1}}
+GRCh37	22	22	89	22	22	89	3to5	17400000	17700000	-29	29	-29	29	.	.	00000000-0000-0000-0000-000000000000	EMBL.DELLYv1.1.3	DEL	DEL	{"""backgroundCarriers""":0,"""affectedCarriers""":0,"""unaffectedCarriers""":0}	0	2	1	0	0	{"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4,"""cn""":2},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":35,"""pec""":0,"""pev""":0,"""src""":29,"""srv""":2,"""cn""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":67,"""pec""":0,"""pev""":0,"""src""":32,"""srv""":1,"""cn""":2}}
diff --git a/...-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java b/...-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java
@@ -67,10 +67,14 @@ public final class AnnotateSvsVcf {
   /** Pedigree to use for annotation. */
   private Pedigree pedigree;
 
+  /** Helper to use for creating genotypes and feature effects files. */
+  private CallerSupport callerSupport;
+
   /** Construct with the given configuration. */
   public AnnotateSvsVcf(AnnotateSvsArgs args) {
     this.args = args;
     this.pedigree = null;
+    this.callerSupport = CallerSupportFactory.getFor(new File(args.getInputVcf()));
   }
 
   /** UUID counter for sequential UUID generation. */
@@ -236,7 +240,8 @@ private void annotateSvVcf(
             args.getOptOutFeatures(),
             args.getCaseId(),
             args.getSetId(),
-            pedigree);
+            pedigree,
+            callerSupport);
     final FeatureEffectsRecordBuilder feRecordBuilder =
         new FeatureEffectsRecordBuilder(args.getCaseId(), args.getSetId());
 

diff --git a/...t/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java b/...t/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateDellyVcf37Chr1Test.java
@@ -172,11 +172,11 @@ void testWithTrio(boolean gzipOutput) throws IOException {
             + "GRCh37\tthousand_genomes\tv5b.20130502\n";
     final String expectedGts =
         "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n"
-            + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":57,\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
-            + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":39,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
-            + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":157,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n"
-            + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"
-            + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n";
+            + "GRCh37\t1\t1\t599\t1\t1\t599\t3to5\t1866283\t1867170\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":57,\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+            + "GRCh37\t1\t1\t604\t1\t1\t604\t5to3\t2583294\t2583895\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t2\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":39,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+            + "GRCh37\t1\t1\t780\t1\t1\t780\t3to3\t25613682\t25614267\t-6\t6\t-6\t6\t.\t.\t00000000-0000-0000-0000-000000000002\tEMBL.DELLYv0.8.5\tINV\tINV\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t0\t3\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":123,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":46,\"\"\"srv\"\"\":7},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":43,\"\"\"srv\"\"\":8},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":157,\"\"\"pec\"\"\":0,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":56,\"\"\"srv\"\"\":8}}\n"
+            + "GRCh37\t14\t14\t1299\t1\t1\t1299\t3to3\t93713177\t93713177\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000003\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"1\"\"\",\"\"\"pos2\"\"\":9121445,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t1\t2\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":39,\"\"\"pev\"\"\":15,\"\"\"src\"\"\":37,\"\"\"srv\"\"\":18}}\n"
+            + "GRCh37\t1\t1\t654\t14\t14\t654\t3to3\t9121445\t9121445\t-3\t3\t-3\t3\t.\t.\t00000000-0000-0000-0000-000000000004\tEMBL.DELLYv0.8.5\tBND\tBND\t{\"\"\"chr2\"\"\":\"\"\"14\"\"\",\"\"\"pos2\"\"\":93713177,\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t0\t3\t0\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":50,\"\"\"pev\"\"\":17,\"\"\"src\"\"\":54,\"\"\"srv\"\"\":21},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":93,\"\"\"pec\"\"\":31,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":31,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":10000,\"\"\"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(
@@ -256,8 +256,8 @@ void testAnnotateHemiFamily() throws Exception {
             + "GRCh37\tthousand_genomes\tv5b.20130502\n";
     final String expectedGts =
         "release\tchromosome\tchromosome_no\tbin\tchromosome2\tchromosome_no2\tbin2\tpe_orientation\tstart\tend\tstart_ci_left\tstart_ci_right\tend_ci_left\tend_ci_right\tcase_id\tset_id\tsv_uuid\tcaller\tsv_type\tsv_sub_type\tinfo\tnum_hom_alt\tnum_hom_ref\tnum_het\tnum_hemi_alt\tnum_hemi_ref\tgenotype\n"
-            + "GRCh37\tX\t23\t592\tX\t23\t592\t3to5\t1000000\t1001000\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t1\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":57,\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
-            + "GRCh37\tX\t23\t607\tX\t23\t607\t5to3\t3000000\t3001000\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t2\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0,\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":39,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n";
+            + "GRCh37\tX\t23\t592\tX\t23\t592\t3to5\t1000000\t1001000\t-56\t56\t-56\t56\t.\t.\t00000000-0000-0000-0000-000000000000\tEMBL.DELLYv0.8.5\tDEL\tDEL\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t1\t1\t0\t0\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":10000,\"\"\"pec\"\"\":22,\"\"\"pev\"\"\":6,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/1\"\"\",\"\"\"gq\"\"\":127,\"\"\"pec\"\"\":11,\"\"\"pev\"\"\":4,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":57,\"\"\"pec\"\"\":19,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n"
+            + "GRCh37\tX\t23\t607\tX\t23\t607\t5to3\t3000000\t3001000\t-624\t624\t-624\t624\t.\t.\t00000000-0000-0000-0000-000000000001\tEMBL.DELLYv0.8.5\tDUP\tDUP\t{\"\"\"backgroundCarriers\"\"\":0,\"\"\"affectedCarriers\"\"\":0,\"\"\"unaffectedCarriers\"\"\":0}\t1\t0\t0\t0\t2\t{\"\"\"NA12878\"\"\":{\"\"\"gt\"\"\":\"\"\"1/1\"\"\",\"\"\"gq\"\"\":80,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":3,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12891\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":24,\"\"\"pec\"\"\":12,\"\"\"pev\"\"\":1,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0},\"\"\"NA12892\"\"\":{\"\"\"gt\"\"\":\"\"\"0/0\"\"\",\"\"\"gq\"\"\":39,\"\"\"pec\"\"\":13,\"\"\"pev\"\"\":0,\"\"\"src\"\"\":0,\"\"\"srv\"\"\":0}}\n";
     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(