Fix AD issue; output validates; hom-refs still get MIN_DP, but that's

true for all ploidies
broadinstitute · Apr 4, 2022 · ca3abf3 · ca3abf3
1 parent 4300329
commit ca3abf3
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Showing 3 changed files with 14,764 additions and 11 deletions.
diff --git a/...va/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java b/...va/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java
@@ -331,16 +331,11 @@ protected GenotypesContext iterateOnGenotypes(final VariantContext vc, final Lis
             final GenotypeBuilder genotypeBuilder = new GenotypeBuilder(g);
             genotypeBuilder.name(name);
             if (isGDBnoCall(g) || g.getAlleles().contains(Allele.NON_REF_ALLELE)) {
-                genotypeBuilder.alleles(GATKVariantContextUtils.noCallAlleles(g.getPloidy()));
+                genotypeBuilder.alleles(GATKVariantContextUtils.noCallAlleles(g.getPloidy())).noGQ();
             }
-            else if (nonRefReturned) {
-                if (g.hasAD()) {
-                    final int[] AD = trimADs(g, targetAlleles.size());
-                    genotypeBuilder.AD(AD);
-                }
-                else if (g.countAllele(Allele.NON_REF_ALLELE) > 0) {
-                    genotypeBuilder.alleles(GATKVariantContextUtils.noCallAlleles(g.getPloidy())).noGQ();
-                }
+            if (nonRefReturned && g.hasAD()) {
+                final int[] AD = trimADs(g, targetAlleles.size());
+                genotypeBuilder.AD(AD);
             }
             if (g.hasPL()) {
                 //lookup PL size from cache if ploidy matches and cache has our number of alts

diff --git a/...test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java b/...test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java
@@ -56,9 +56,9 @@ public void assertThatExpectedOutputUpdateToggleIsDisabled() {
     @DataProvider(name="VCFdata")
     public Object[][] getVCFdata() {
         return new Object[][]{
-                //chrX haploid sample plus diploid sample
+                //chrX haploid sample plus diploid sample -- expected results validated with vcf-validator (samtools?)
                 {new File[]{getTestFile("NA12891.chrX.haploid.rb.g.vcf"), getTestFile("NA12892.chrX.diploid.rb.g.vcf")},
-                        getTestFile("lotsOfAltsNoPLs.vcf"), null, Arrays.asList(new SimpleInterval("chrX", 1000000, 5000000)), Arrays.asList("--merge-input-intervals", "--only-output-calls-starting-in-intervals"), b38_reference_20_21},
+                        getTestFile("haploidPlusDiploid.expected.vcf"), null, Arrays.asList(new SimpleInterval("chrX", 1000000, 5000000)), Arrays.asList("--merge-input-intervals", "--only-output-calls-starting-in-intervals"), b38_reference_20_21},
 
                 //8 ALT alleles -- no PLs
                 {new File[]{getTestFile("sample6.vcf"), getTestFile("sample7.vcf"), getTestFile("sample8.vcf"), getTestFile("sample9.vcf")},