From 9684a2efb0f8593b4546e39701e99c4212120f26 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 29 Mar 2012 09:41:29 -0400 Subject: [PATCH] HaplotypeCaller: Variants found on the same haplotype are now written out with phased genotypes. There are serious eval issues with MNPs so disabling them for now. --- .../sting/gatk/walkers/varianteval/evaluators/CompOverlap.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index 2715b383b..8ef362ba5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; */ @Analysis(description = "The overlap between eval and comp sites") public class CompOverlap extends VariantEvaluator implements StandardEval { - @DataPoint(description = "number of eval SNP sites", format = "%d") + @DataPoint(description = "number of eval variant sites", format = "%d") long nEvalVariants = 0; @DataPoint(description = "number of eval sites outside of comp sites", format = "%d")