HOM Reference and tumor should have vaf 1

hartwigmedical · Mar 15, 2021 · 2440290 · 2440290
1 parent 33b6c16
commit 2440290
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/...on/src/main/java/com/hartwig/hmftools/common/variant/enrich/GermlinePurityEnrichment.java b/...on/src/main/java/com/hartwig/hmftools/common/variant/enrich/GermlinePurityEnrichment.java
@@ -61,7 +61,7 @@ public void accept(@NotNull final VariantContext variant) {
             if (optionalPurpleCopyNumber.isPresent()) {
                 PurpleCopyNumber purpleCopyNumber = optionalPurpleCopyNumber.get();
                 double copyNumber = purpleCopyNumber.averageTumorCopyNumber();
-                double vaf = vaf(germlineGenotype, purpleCopyNumber, tumorDepth);
+                double vaf = germlineGenotype == GenotypeStatus.HOM_ALT ? 1.0 : vaf(germlineGenotype, purpleCopyNumber, tumorDepth);
                 double variantCopyNumber = Math.max(0, vaf * copyNumber);
                 boolean biallelic = Doubles.lessOrEqual(copyNumber, 0) || Doubles.greaterOrEqual(variantCopyNumber, copyNumber - 0.5);