From 4ac636e28897f423031c1f7e6aab7e07c1584455 Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 14 Oct 2010 01:35:33 +0000 Subject: [PATCH] Minor change: when tabulating concordance by AC, ignore sites with multiple segregating alleles in the population, at least for now git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4493 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/varianteval/GenotypeConcordance.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java index 1f3712a4a..6bb5fe16e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java @@ -297,8 +297,8 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva String interesting = null; final boolean validationIsValidVC = isValidVC(validation); - final String evalAC = (eval != null && eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) ? String.format("evalAC%s",eval.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null ; - final String validationAC = ( validationIsValidVC && validation.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) ? String.format("compAC%s",validation.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null; + final String evalAC = (eval != null && eval.getAlternateAlleles().size() == 1 && eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) ? String.format("evalAC%s",eval.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null ; + final String validationAC = ( validationIsValidVC && validation.getAlternateAlleles().size() == 1 && validation.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) ? String.format("compAC%s",validation.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null; // determine concordance for eval data if (eval != null) {