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 e1c415183..c4ecd3580 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +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; @@ -87,6 +88,12 @@ public class VariantsToTable extends RodWalker { } }); getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } }); + getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) { + if ( vc.isSNP() && vc.isBiallelic() ) + return VariantContextUtils.isTransition(vc) ? "1" : "0"; + else + return "-1"; + }}); getters.put("FILTER", new Getter() { public String get(VariantContext vc) { return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); } });