Fix sites with zero AD to actually use SITE-level DP value as intende…

…d in (#5835)
broadinstitute · Mar 27, 2019 · 2b3898c · 2b3898c
1 parent b7f90f4
commit 2b3898c
Show file tree

Hide file tree

Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
@@ -354,7 +354,7 @@ protected VariantContext cleanUpHighQualityVariant(final VariantContext result,
             attrMap.put(GATKVCFConstants.RAW_QUAL_APPROX_KEY, genotype.getPL()[0]);
             int varDP = QualByDepth.getDepth(result.getGenotypes(), null);
             if (varDP == 0) {  //prevent QD=Infinity case
-                varDP = result.getAttributeAsInt(VCFConstants.DEPTH_KEY, 1); //if there's no VarDP and no DP, just prevent Infs/NaNs and QD will get capped later
+                varDP = originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 1); //if there's no VarDP and no DP, just prevent Infs/NaNs and QD will get capped later
             }
             attrMap.put(GATKVCFConstants.VARIANT_DEPTH_KEY, varDP);
         }

diff --git a/.../broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/gvcfForReblocking.g.vcf b/.../broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/gvcfForReblocking.g.vcf
@@ -30,6 +30,6 @@ chr20	69635	.	A	T,<NON_REF>	60.77	.	BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRan
 chr20	69762	.	A	<NON_REF>	.	.	BLOCK_SIZE=1;END=69762	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:18:7:18:0,18,270
 chr20	69763	.	A	<NON_REF>	.	.	BLOCK_SIZE=4;END=69766	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:21:7:21:0,21,253
 chr20	69767	.	A	<NON_REF>	.	.	BLOCK_SIZE=4;END=69770	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:12:7:12:0,12,180
-chr20	69771	.	TAAAAA	T,<NON_REF>	60.77	.	BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:20:20,0,119,101,128,229:0,4,0,3
+chr20	69771	.	TAAAAA	T,<NON_REF>	60.77	.	BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:0,0,0:0:20:20,0,119,101,128,229:0,4,0,3
 chr20	69777	.	G	<NON_REF>	.	.	BLOCK_SIZE=10;END=69783	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:0:3:0:0,0,0
 chr20	69785	.	T	G,<NON_REF>	2253.77	.	BaseQRankSum=1.169;DP=82;MQ=31.05;MQ0=0;MQRankSum=-0.866;ReadPosRankSum=1.689	GT:DP:GQ:PL:SB	1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33
diff --git a/...titute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf b/...titute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf
@@ -32,6 +32,6 @@ chr20	69522	.	A	<NON_REF>	.	.	END=69635	GT:DP:GQ:MIN_DP:PL	0/0:7:0:6:0,0,0
 chr20	69762	.	A	<NON_REF>	.	.	END=69762	GT:DP:GQ:MIN_DP:PL	0/0:7:18:7:0,18,270
 chr20	69763	.	A	<NON_REF>	.	.	END=69766	GT:DP:GQ:MIN_DP:PL	0/0:7:21:7:0,21,253
 chr20	69767	.	A	<NON_REF>	.	.	END=69770	GT:DP:GQ:MIN_DP:PL	0/0:7:12:7:0,12,180
-chr20	69771	.	TAAAAA	T,<NON_REF>	12.59	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;RAW_MQandDP=239.05,7;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:20:20,0,119,101,128,229:0,4,0,3
+chr20	69771	.	TAAAAA	T,<NON_REF>	12.59	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;RAW_MQandDP=239.05,7;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:0,0,0:0:20:20,0,119,101,128,229:0,4,0,3
 chr20	69777	.	G	<NON_REF>	.	.	END=69783	GT:DP:GQ:MIN_DP:PL	0/0:7:0:7:0,0,0
 chr20	69785	.	T	G,<NON_REF>	2270.03	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;RAW_MQandDP=2546.10,82;ReadPosRankSum=1.689	GT:DP:GQ:PL:SB	1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33
diff --git a/...hellbender/tools/walkers/variantutils/ReblockGVCF/testOneSampleAsForGnomAD.expected.g.vcf b/...hellbender/tools/walkers/variantutils/ReblockGVCF/testOneSampleAsForGnomAD.expected.g.vcf
@@ -33,5 +33,5 @@ chr20	69635	.	A	T,<NON_REF>	2.64	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;QUALapp
 chr20	69762	.	A	<NON_REF>	.	.	END=69762	GT:DP:GQ:MIN_DP:PL	0/0:7:18:7:0,18,270
 chr20	69763	.	A	<NON_REF>	.	.	END=69766	GT:DP:GQ:MIN_DP:PL	0/0:7:21:7:0,21,253
 chr20	69767	.	A	<NON_REF>	.	.	END=69770	GT:DP:GQ:MIN_DP:PL	0/0:7:12:7:0,12,180
-chr20	69771	.	TAAAAA	T,<NON_REF>	12.59	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;QUALapprox=20;RAW_MQandDP=239.05,7;ReadPosRankSum=1.754;VarDP=7	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:20:20,0,119,101,128,229:0,4,0,3
+chr20	69771	.	TAAAAA	T,<NON_REF>	12.59	.	DP=7;MQ=34.15;MQRankSum=1.300;MQ_DP=7;QUALapprox=20;RAW_MQandDP=239.05,7;ReadPosRankSum=1.754;VarDP=7	GT:AD:DP:GQ:PL:SB	0/1:0,0,0:0:20:20,0,119,101,128,229:0,4,0,3
 chr20	69785	.	T	G,<NON_REF>	2270.03	.	DP=82;MQ=31.05;MQRankSum=-0.866;MQ_DP=82;QUALapprox=2284;RAW_MQandDP=2546.10,82;ReadPosRankSum=1.689;VarDP=80	GT:DP:GQ:PL:SB	1/1:80:99:2284,207,0,2287,237,2316:0,1,46,33