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Two new annotations: 

1. LowMQ: fraction of reads at MQ=0 or MQ<=10.
	2. Alignability: annotate SNPs with Heng's (or anyone else's) alignability mask.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2746 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2010-01-29 23:23:00 +00:00
parent 97f60dbc4b
commit ea7e737441
2 changed files with 75 additions and 0 deletions
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39
java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java 100755
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package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.TabularROD;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
public class Alignability implements VariantAnnotation {
public String annotate(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, StratifiedAlignmentContext> stratifiedContexts,
Variation variation)
{
TabularROD record = (TabularROD)(tracker.lookup("alignability", null));
int value;
if (record == null) { value = 3; }
else
{
if (record.get("alignability") == null)
{
throw new RuntimeException("ERROR: alignability column not defined in alignability input.\n");
}
value = Integer.parseInt(record.get("alignability"));
}
return String.format("%d", value);
}
public String getKeyName() { return "Alignability"; }
public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(getKeyName(), 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Alignability according to a mask file (3 is best, 0 is worst)"); }
}

36
java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java 100755
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package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
import java.util.Map;
public class LowMQ implements VariantAnnotation {
public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
double mq0 = 0;
double mq10 = 0;
double total = 0;
for ( String sample : stratifiedContexts.keySet() )
{
ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
for (PileupElement p : pileup )
{
if ( p.getMappingQual() == 0 ) { mq0 += 1; }
if ( p.getMappingQual() <= 10 ) { mq10 += 1; }
total += 1;
}
}
return String.format("%.04f,%.04f,%.00f", mq0/total, mq10/total, total);
}
public String getKeyName() { return "LowMQ"; }
public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(getKeyName(), 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "3-tuple: <fraction of reads with MQ=0>,<fraction of reads with MQ<=10>,<total nubmer of reads>"); }
}