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

Closes: #68
Closes: #60
Related-Issue: #68
Projected-Results-Impact: none

README.md

@@ -43,9 +43,26 @@ 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.
+
+- Delly 2 (SVs)
+- Dragen CNV caller
+- Dragen SV caller
+- Manta
+- GATK gCNV
+- XHMM (deprecated)
+
+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.
+Your caller should also write out `INFO/END`, `INFO/SVTYPE`, and `INFO/SVLEN` as defined by VCF4.2
+
+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 +87,32 @@ 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
 

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	.	.	UUID	EMBL.DELLYv1.1.3	DEL	DEL	{"""backgroundCarriers""":0,"""affectedCarriers""":0,"""unaffectedCarriers""":0}	0	2	1	0	0	{"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ft""":{"""LowQual"""},"""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4,"""cn""":2},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":35,"""pec""":0,"""pev""":0,"""src""":29,"""srv""":2,"""cn""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":67,"""pec""":0,"""pev""":0,"""src""":32,"""srv""":1,"""cn""":2}}

varfish-annotator-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());