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Merge pull request #399 from broadinstitute/eb_update_docs_for_DepthPerSampleHC 

Updated docs for DepthPerSampleHC to deliver PT #54237024.
This commit is contained in:
Geraldine Van der Auwera 2013-09-25 15:20:19 -07:00
parent f362597f69 2783c84c6b
commit a9fa5206ee
1 changed files with 9 additions and 6 deletions
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15
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
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@ -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<VCFFormatHeaderLine> getDescriptions() {
return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY));
}
}