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Fix GGVCFs typo #8742

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Fix GGVCFs typo #8742

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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@ private VariantContext regenotypeVC(final VariantContext originalVC, final Refer
//don't count sites with no depth and no confidence towards things like AN and InbreedingCoeff
vcBuilder.genotypes(assignNoCallsAnnotationExcludedGenotypes(result.getGenotypes()));
VariantContext annotated = annotationEngine.annotateContext(vcBuilder.make(), features, ref, null, a -> true);
return new VariantContextBuilder(annotated).genotypes(cleanupGenotypeAnnotations(result, false, keepSB)).make();
return new VariantContextBuilder(annotated).genotypes(cleanupGenotypeAnnotations(annotated, false, keepSB)).make();
} else if (includeNonVariants) {
// For monomorphic sites we need to make sure e.g. the hom ref genotypes are created and only then are passed to the annotation engine.
VariantContext preannotated = new VariantContextBuilder(result).genotypes(cleanupGenotypeAnnotations(result, true, false)).make();
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