zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding a hidden (for now) argument to UG (and HC) that tells the caller that the incoming samples are contaminated by N% and to fix it by aggressively down-sampling all alleles. This actually works. Yes, you read that right: given that we know what N is, we can make good calls on bams that have N% contamination. Only hooked up for SNPS right now. No tests added yet.

This commit is contained in:
Eric Banks 2012-10-20 23:31:56 -04:00
parent 2c624f76c8
commit 841a906f21
1 changed files with 60 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

67
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -41,19 +41,20 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.*;
public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
private final boolean useAlleleFromVCF;
private final double[] likelihoodSums = new double[4];
private final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
super(UAC, logger);
useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
for ( int i = 0; i < 4; i++ )
alleleStratifiedElements[i] = new ArrayList<PileupElement>();
}
public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
@ -78,8 +79,10 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
ArrayList<SampleGenotypeData> GLs = new ArrayList<SampleGenotypeData>(contexts.size());
for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {
ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();
if ( UAC.CONTAMINATION_PERCENTAGE > 0.0 )
pileup = createDecontaminatedPileup(pileup, UAC.CONTAMINATION_PERCENTAGE);
if ( useBAQedPileup )
pileup = createBAQedPileup( pileup );
pileup = createBAQedPileup(pileup);
// create the GenotypeLikelihoods object
final DiploidSNPGenotypeLikelihoods GL = new DiploidSNPGenotypeLikelihoods(UAC.PCR_error);
@ -150,8 +153,6 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
// create the genotypes; no-call everyone for now
final GenotypesContext genotypes = GenotypesContext.create();
final List<Allele> noCall = new ArrayList<Allele>();
noCall.add(Allele.NO_CALL);
for ( SampleGenotypeData sampleData : GLs ) {
final double[] allLikelihoods = sampleData.GL.getLikelihoods();
@ -202,6 +203,42 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
return allelesToUse;
}
public ReadBackedPileup createDecontaminatedPileup(final ReadBackedPileup pileup, final double contaminationPercentage) {
// special case removal of all reads
if ( contaminationPercentage >= 1.0 )
return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>());
// start by stratifying the reads by the alleles they represent at this position
for( final PileupElement pe : pileup ) {
final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase());
if ( baseIndex != -1 )
alleleStratifiedElements[baseIndex].add(pe);
}
// Down-sample *each* allele by the contamination fraction applied to the entire pileup.
// Unfortunately, we need to maintain the original pileup ordering of reads or FragmentUtils will complain later.
int numReadsToRemove = (int)Math.ceil((double)pileup.getNumberOfElements() * contaminationPercentage);
final TreeSet<PileupElement> elementsToKeep = new TreeSet<PileupElement>(new Comparator<PileupElement>() {
@Override
public int compare(PileupElement element1, PileupElement element2) {
final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart();
return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
}
});
for ( int i = 0; i < 4; i++ ) {
final ArrayList<PileupElement> alleleList = alleleStratifiedElements[i];
if ( alleleList.size() > numReadsToRemove )
elementsToKeep.addAll(downsampleElements(alleleList, numReadsToRemove));
}
// clean up pointers so memory can be garbage collected if needed
for ( int i = 0; i < 4; i++ )
alleleStratifiedElements[i].clear();
return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>(elementsToKeep));
}
public ReadBackedPileup createBAQedPileup( final ReadBackedPileup pileup ) {
final List<PileupElement> BAQedElements = new ArrayList<PileupElement>();
for( final PileupElement PE : pileup ) {
@ -220,6 +257,22 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
public byte getQual( final int offset ) { return BAQ.calcBAQFromTag(getRead(), offset, true); }
}
private List<PileupElement> downsampleElements(final ArrayList<PileupElement> elements, final int numElementsToRemove) {
final int pileupSize = elements.size();
final BitSet itemsToRemove = new BitSet(pileupSize);
for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) {
itemsToRemove.set(selectedIndex);
}
ArrayList<PileupElement> elementsToKeep = new ArrayList<PileupElement>(pileupSize - numElementsToRemove);
for ( int i = 0; i < pileupSize; i++ ) {
if ( !itemsToRemove.get(i) )
elementsToKeep.add(elements.get(i));
}
return elementsToKeep;
}
private static class SampleGenotypeData {
public final String name;