diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java index 9bd641011..21325e6f1 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java @@ -51,7 +51,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -68,11 +67,15 @@ import java.util.*; /** - * The depth of coverage of each allele per sample + * The depth of coverage for informative reads for each sample. * - * the depth for the HC is the sum of the informative alleles at this site. It's not perfect (as we cannot - * differentiate between reads that align over the event but aren't informative vs. those that aren't even - * close) but it's a pretty good proxy and it matches with the AD field (i.e., sum(AD) = DP). + * An informative read is defined as one from which the allele it carries can be easily distinguished. An example of a + * case where a read might be uninformative is where it only partially overlaps a short tandem repeat and it is not clear + * whether the read contains the reference allele or e.g. an extra repeat. + * The depth here is the sum of the informative reads at this site as determined by the Haplotype Caller; as such it can + * only be calculated and generated through the Haplotype Caller (it will not work when run through the Variant Annotator). + * This calculation is not perfect but it is a pretty good proxy for depth and it does match the values in the AD field + * (i.e., sum(AD) = DP). */ public class DepthPerSampleHC extends GenotypeAnnotation { public void annotate(final RefMetaDataTracker tracker, @@ -121,6 +124,6 @@ public class DepthPerSampleHC extends GenotypeAnnotation { } public List getDescriptions() { - return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0))); + return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY)); } } \ No newline at end of file