From 57c66b5602ab10c63eecdbd255153b9bf8c054d8 Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 17 Feb 2011 22:30:25 +0000 Subject: [PATCH] Supports GQ now git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5265 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/variantutils/VariantsToTable.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 7b4d05130..944612c44 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -33,7 +33,9 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.PrintStream; import java.util.*; @@ -103,6 +105,10 @@ public class VariantsToTable extends RodWalker { getters.put("VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount() + vc.getHomVarCount()); } }); getters.put("NSAMPLES", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples()); } }); getters.put("NCALLED", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples() - vc.getNoCallCount()); } }); + getters.put("GQ", new Getter() { public String get(VariantContext vc) { + if ( vc.getNSamples() > 1 ) throw new UserException("Cannot get GQ values for multi-sample VCF"); + return String.format("%.2f", 10 * vc.getGenotype(0).getNegLog10PError()); + }}); }