Improvements to indel calling in pool caller: a) Compute per-read likelihoods in reference sample to determine wheter a read is informative or not. b) Fixed bugs in unit tests. c) Fixed padding-related bugs when computing matches/mismatches in ErrorModel, d) Added a couple of more integration tests to increase test coverage, including testing odd ploidy
This commit is contained in:
Guillermo del Angel
parent
1e8610b2c6
commit
2ae890155c
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@ -1,6 +1,10 @@
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package org.broadinstitute.sting.gatk.walkers.genotyper;
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import com.google.java.contract.Requires;
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import org.apache.commons.lang.ArrayUtils;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
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import org.broadinstitute.sting.utils.Haplotype;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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@ -9,6 +13,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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/**
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* Created by IntelliJ IDEA.
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@ -30,24 +35,26 @@ public class ErrorModel {
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private static final boolean compressRange = false;
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private static final double log10MinusE = Math.log10(Math.exp(1.0));
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private static final boolean DEBUG = false;
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/**
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* Calculates the probability of the data (reference sample reads) given the phred scaled site quality score.
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*
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* @param minQualityScore Minimum site quality score to evaluate
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* @param maxQualityScore Maximum site quality score to evaluate
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* @param phredScaledPrior Prior for site quality
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* @param UAC Argument Collection
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* @param refSamplePileup Reference sample pileup
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* @param refSampleVC VC with True alleles in reference sample pileup
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* @param minPower Minimum power
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*/
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public ErrorModel (byte minQualityScore, byte maxQualityScore, byte phredScaledPrior,
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ReadBackedPileup refSamplePileup, VariantContext refSampleVC, double minPower) {
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this.maxQualityScore = maxQualityScore;
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this.minQualityScore = minQualityScore;
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this.phredScaledPrior = phredScaledPrior;
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log10minPower = Math.log10(minPower);
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public ErrorModel (final UnifiedArgumentCollection UAC,
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final ReadBackedPileup refSamplePileup,
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VariantContext refSampleVC, final ReferenceContext refContext) {
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this.maxQualityScore = UAC.maxQualityScore;
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this.minQualityScore = UAC.minQualityScore;
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this.phredScaledPrior = UAC.phredScaledPrior;
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log10minPower = Math.log10(UAC.minPower);
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PairHMMIndelErrorModel pairModel = null;
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LinkedHashMap<Allele, Haplotype> haplotypeMap = null;
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HashMap<PileupElement, LinkedHashMap<Allele, Double>> indelLikelihoodMap = null;
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double[][] perReadLikelihoods = null;
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double[] model = new double[maxQualityScore+1];
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Arrays.fill(model,Double.NEGATIVE_INFINITY);
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@ -61,11 +68,17 @@ public class ErrorModel {
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break;
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}
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}
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if (refSampleVC.isIndel()) {
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pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY, UAC.INDEL_GAP_CONTINUATION_PENALTY,
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UAC.OUTPUT_DEBUG_INDEL_INFO, !UAC.DONT_DO_BANDED_INDEL_COMPUTATION);
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haplotypeMap = new LinkedHashMap<Allele, Haplotype>();
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indelLikelihoodMap = new HashMap<PileupElement, LinkedHashMap<Allele, Double>>();
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IndelGenotypeLikelihoodsCalculationModel.getHaplotypeMapFromAlleles(refSampleVC.getAlleles(), refContext, refContext.getLocus(), haplotypeMap); // will update haplotypeMap adding elements
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}
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}
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double p = MathUtils.phredScaleToLog10Probability((byte)(maxQualityScore-minQualityScore));
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if (refSamplePileup == null || refSampleVC == null || !hasCalledAlleles) {
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double p = MathUtils.phredScaleToLog10Probability((byte)(maxQualityScore-minQualityScore));
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for (byte q=minQualityScore; q<=maxQualityScore; q++) {
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// maximum uncertainty if there's no ref data at site
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model[q] = p;
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@ -75,23 +88,47 @@ public class ErrorModel {
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else {
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hasData = true;
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int matches = 0;
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int coverage = refSamplePileup.getNumberOfElements();
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int coverage = 0;
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Allele refAllele = refSampleVC.getReference();
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if (refSampleVC.isIndel()) {
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final int readCounts[] = new int[refSamplePileup.getNumberOfElements()];
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//perReadLikelihoods = new double[readCounts.length][refSampleVC.getAlleles().size()];
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final int eventLength = IndelGenotypeLikelihoodsCalculationModel.getEventLength(refSampleVC.getAlleles());
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perReadLikelihoods = pairModel.computeGeneralReadHaplotypeLikelihoods(refSamplePileup,haplotypeMap,refContext, eventLength, indelLikelihoodMap, readCounts);
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}
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int idx = 0;
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for (PileupElement refPileupElement : refSamplePileup) {
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if (DEBUG)
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System.out.println(refPileupElement.toString());
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boolean isMatch = false;
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for (Allele allele : refSampleVC.getAlleles())
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isMatch |= pileupElementMatches(refPileupElement, allele, refAllele);
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for (Allele allele : refSampleVC.getAlleles()) {
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boolean m = pileupElementMatches(refPileupElement, allele, refAllele, refContext.getBase());
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if (DEBUG) System.out.println(m);
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isMatch |= m;
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}
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if (refSampleVC.isIndel()) {
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// ignore match/mismatch if reads, as determined by their likelihood, are not informative
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double[] perAlleleLikelihoods = perReadLikelihoods[idx++];
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if (!isInformativeElement(perAlleleLikelihoods))
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matches++;
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else
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matches += (isMatch?1:0);
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matches += (isMatch?1:0);
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// System.out.format("MATCH:%b\n",isMatch);
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} else {
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matches += (isMatch?1:0);
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}
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coverage++;
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}
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int mismatches = coverage - matches;
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//System.out.format("Cov:%d match:%d mismatch:%d\n",coverage, matches, mismatches);
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for (byte q=minQualityScore; q<=maxQualityScore; q++) {
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model[q] = log10PoissonProbabilitySiteGivenQual(q,coverage, mismatches);
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if (coverage==0)
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model[q] = p;
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else
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model[q] = log10PoissonProbabilitySiteGivenQual(q,coverage, mismatches);
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}
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this.refDepth = coverage;
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}
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@ -101,6 +138,17 @@ public class ErrorModel {
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}
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@Requires("likelihoods.length>0")
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private boolean isInformativeElement(double[] likelihoods) {
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// if likelihoods are the same, they're not informative
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final double thresh = 0.1;
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int maxIdx = MathUtils.maxElementIndex(likelihoods);
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int minIdx = MathUtils.minElementIndex(likelihoods);
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if (likelihoods[maxIdx]-likelihoods[minIdx]< thresh)
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return false;
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else
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return true;
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}
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/**
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* Simple constructor that just takes a given log-probability vector as error model.
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* Only intended for unit testing, not general usage.
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@ -115,23 +163,27 @@ public class ErrorModel {
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}
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public static boolean pileupElementMatches(PileupElement pileupElement, Allele allele, Allele refAllele) {
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/* System.out.format("PE: base:%s isNextToDel:%b isNextToIns:%b eventBases:%s eventLength:%d Allele:%s RefAllele:%s\n",
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public static boolean pileupElementMatches(PileupElement pileupElement, Allele allele, Allele refAllele, byte refBase) {
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if (DEBUG)
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System.out.format("PE: base:%s isNextToDel:%b isNextToIns:%b eventBases:%s eventLength:%d Allele:%s RefAllele:%s\n",
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pileupElement.getBase(), pileupElement.isBeforeDeletionStart(),
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pileupElement.isBeforeInsertion(),pileupElement.getEventBases(),pileupElement.getEventLength(), allele.toString(), refAllele.toString());
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*/
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//pileupElement.
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// if test allele is ref, any base mismatch, or any insertion/deletion at start of pileup count as mismatch
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if (allele.isReference()) {
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// for a ref allele, any base mismatch or new indel is a mismatch.
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if(allele.getBases().length>0 && allele.getBases().length == refAllele.getBases().length ) // SNP/MNP case
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return (/*!pileupElement.isBeforeInsertion() && !pileupElement.isBeforeDeletionStart() &&*/ pileupElement.getBase() == allele.getBases()[0]);
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if(allele.getBases().length>0 )
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// todo - can't check vs. allele because allele is not padded so it doesn't include the reference base at this location
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// could clean up/simplify this when unpadding is removed
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return (pileupElement.getBase() == refBase);
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else
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// either null allele to compare, or ref/alt lengths are different (indel by definition).
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// if we have an indel that we are comparing against a REF allele, any indel presence (of any length/content) is a mismatch
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return (!pileupElement.isBeforeInsertion() && !pileupElement.isBeforeDeletionStart());
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}
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// for non-ref alleles to compare:
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if (refAllele.getBases().length == allele.getBases().length)
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// alleles have the same length (eg snp or mnp)
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return pileupElement.getBase() == allele.getBases()[0];
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@ -247,7 +247,8 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
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// find the alternate allele(s) that we should be using
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final List<Allele> alleles = getFinalAllelesToUse(tracker, ref, allAllelesToUse, GLs);
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if (alleles == null || alleles.isEmpty())
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return null;
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// start making the VariantContext
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final GenomeLoc loc = ref.getLocus();
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final int endLoc = getEndLocation(tracker, ref, alleles);
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@ -313,7 +314,7 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
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refLanePileup = refPileup.getPileupForLane(laneID);
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//ReferenceSample referenceSample = new ReferenceSample(UAC.referenceSampleName, refLanePileup, trueReferenceAlleles);
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perLaneErrorModels.put(laneID, new ErrorModel(UAC.minQualityScore, UAC.maxQualityScore, UAC.phredScaledPrior, refLanePileup, refVC, UAC.minPower));
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perLaneErrorModels.put(laneID, new ErrorModel(UAC, refLanePileup, refVC, ref));
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}
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return perLaneErrorModels;
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@ -25,6 +25,8 @@ public class PoolIndelGenotypeLikelihoods extends PoolGenotypeLikelihoods {
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final int eventLength;
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double[][] readHaplotypeLikelihoods;
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final byte refBase;
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public PoolIndelGenotypeLikelihoods(final List<Allele> alleles,
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final double[] logLikelihoods,
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final int ploidy,
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@ -38,6 +40,8 @@ public class PoolIndelGenotypeLikelihoods extends PoolGenotypeLikelihoods {
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this.haplotypeMap = haplotypeMap;
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this.refContext = referenceContext;
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this.eventLength = IndelGenotypeLikelihoodsCalculationModel.getEventLength(alleles);
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// todo - not needed if indel alleles have base at current position
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this.refBase = referenceContext.getBase();
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}
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// -------------------------------------------------------------------------------------
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@ -141,7 +145,7 @@ public class PoolIndelGenotypeLikelihoods extends PoolGenotypeLikelihoods {
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final int numHaplotypes = haplotypeMap.size();
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final int readCounts[] = new int[pileup.getNumberOfElements()];
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readHaplotypeLikelihoods = pairModel.computeGeneralReadHaplotypeLikelihoods(pileup, haplotypeMap, refContext, eventLength, PoolIndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap(), readCounts);
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readHaplotypeLikelihoods = pairModel.computeGeneralReadHaplotypeLikelihoods(pileup, haplotypeMap, refContext, eventLength, IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap(), readCounts);
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n = readHaplotypeLikelihoods.length;
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} else {
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Allele refAllele = null;
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@ -161,7 +165,7 @@ public class PoolIndelGenotypeLikelihoods extends PoolGenotypeLikelihoods {
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int idx =0;
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for (Allele allele : alleles) {
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int cnt = numSeenBases.get(idx);
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numSeenBases.set(idx++,cnt + (ErrorModel.pileupElementMatches(elt, allele, refAllele)?1:0));
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numSeenBases.set(idx++,cnt + (ErrorModel.pileupElementMatches(elt, allele, refAllele, refBase)?1:0));
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}
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n++;
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@ -70,12 +70,6 @@ public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLi
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}
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public static HashMap<PileupElement, LinkedHashMap<Allele, Double>> getIndelLikelihoodMap() {
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return IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
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}
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protected PoolGenotypeLikelihoods getPoolGenotypeLikelihoodObject(final List<Allele> alleles,
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final double[] logLikelihoods,
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final int ploidy,
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@ -37,6 +37,13 @@ public class PoolCallerIntegrationTest extends WalkerTest {
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executeTest("testPoolCaller:"+name+" args=" + args, spec);
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}
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private void PC_LSV_Test_NoRef(String args, String name, String model, String md5) {
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final String base = String.format("-T UnifiedGenotyper -R %s -I %s -L %s -glm %s -ignoreLane -pnrm POOL",
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REF, LSV_BAM, LSVINTERVALS, model) + " --no_cmdline_in_header -o %s";
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final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
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executeTest("testPoolCaller:"+name+" args=" + args, spec);
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}
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@Test
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public void testBOTH_GGA_Pools() {
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PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","POOLBOTH","36b8db57f65be1cc3d2d9d7f9f3f26e4");
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@ -44,7 +51,17 @@ public class PoolCallerIntegrationTest extends WalkerTest {
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@Test
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public void testINDEL_GGA_Pools() {
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PC_LSV_Test(String.format(" -maxAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","POOLINDEL","d1339990291648495bfcf4404f051478");
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PC_LSV_Test(String.format(" -maxAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","POOLINDEL","d1339990291648495bfcf4404f051478");
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}
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@Test
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public void testINDEL_maxAlleles2_ploidy3_Pools_noRef() {
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PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","POOLINDEL","b66e7150603310fd57ee7bf9fc590706");
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}
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@Test
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public void testINDEL_maxAlleles2_ploidy1_Pools_noRef() {
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PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","POOLINDEL","ccdae3fc4d2c922f956a186aaad51c29");
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}
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@Test
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
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import net.sf.samtools.SAMUtils;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.MathUtils;
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@ -49,6 +50,13 @@ public class PoolGenotypeLikelihoodsUnitTest {
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private static final boolean SIMULATE_NOISY_PILEUP = false;
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private static final int NUM_SIMULATED_OBS = 10;
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void PoolGenotypeLikelihoodsUnitTest() {
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UAC.minQualityScore = 5;
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UAC.maxQualityScore = 40;
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UAC.phredScaledPrior = (byte)20;
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UAC.minPower = 0.0;
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}
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@Test
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public void testStoringLikelihoodElements() {
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@ -251,8 +259,6 @@ public class PoolGenotypeLikelihoodsUnitTest {
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@Test
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public void testErrorModel() {
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final ArtificialReadPileupTestProvider refPileupTestProvider = new ArtificialReadPileupTestProvider(1,"ref");
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final byte minQ = 5;
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final byte maxQ = 40;
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final byte refByte = refPileupTestProvider.getRefByte();
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final byte altByte = refByte == (byte)'T'? (byte) 'C': (byte)'T';
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final String refSampleName = refPileupTestProvider.getSampleNames().get(0);
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@ -270,7 +276,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
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// get artificial alignment context for ref sample - no noise
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Map<String,AlignmentContext> refContext = refPileupTestProvider.getAlignmentContextFromAlleles(0, new String(new byte[]{altByte}), new int[]{matches, mismatches}, false, 30);
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final ReadBackedPileup refPileup = refContext.get(refSampleName).getBasePileup();
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final ErrorModel emodel = new ErrorModel(minQ,maxQ, (byte)20, refPileup, refVC, 0.0);
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final ErrorModel emodel = new ErrorModel(UAC, refPileup, refVC, refPileupTestProvider.getReferenceContext());
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final double[] errorVec = emodel.getErrorModelVector().getProbabilityVector();
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final double mlEst = -10.0*Math.log10((double)mismatches/(double)(matches+mismatches));
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@ -287,8 +293,6 @@ public class PoolGenotypeLikelihoodsUnitTest {
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@Test
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public void testIndelErrorModel() {
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final ArtificialReadPileupTestProvider refPileupTestProvider = new ArtificialReadPileupTestProvider(1,"ref");
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final byte minQ = 5;
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final byte maxQ = 40;
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final byte refByte = refPileupTestProvider.getRefByte();
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final String altBases = "TCA";
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final String refSampleName = refPileupTestProvider.getSampleNames().get(0);
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@ -313,7 +317,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
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// Ref sample has TC insertion but pileup will have TCA inserted instead to test mismatches
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Map<String,AlignmentContext> refContext = refPileupTestProvider.getAlignmentContextFromAlleles(altBases.length(), altBases, new int[]{matches, mismatches}, false, 30);
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final ReadBackedPileup refPileup = refContext.get(refSampleName).getBasePileup();
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final ErrorModel emodel = new ErrorModel(minQ,maxQ, (byte)20, refPileup, refInsertionVC, 0.0);
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final ErrorModel emodel = new ErrorModel(UAC, refPileup, refInsertionVC, refPileupTestProvider.getReferenceContext());
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final double[] errorVec = emodel.getErrorModelVector().getProbabilityVector();
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final double mlEst = -10.0*Math.log10((double)mismatches/(double)(matches+mismatches));
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||||
|
|
@ -343,7 +347,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
|
|||
// Ref sample has 4bp deletion but pileup will have 3 bp deletion instead to test mismatches
|
||||
Map<String,AlignmentContext> refContext = refPileupTestProvider.getAlignmentContextFromAlleles(-delLength+1, altBases, new int[]{matches, mismatches}, false, 30);
|
||||
final ReadBackedPileup refPileup = refContext.get(refSampleName).getBasePileup();
|
||||
final ErrorModel emodel = new ErrorModel(minQ,maxQ, (byte)20, refPileup, refDeletionVC, 0.0);
|
||||
final ErrorModel emodel = new ErrorModel(UAC, refPileup, refDeletionVC, refPileupTestProvider.getReferenceContext());
|
||||
final double[] errorVec = emodel.getErrorModelVector().getProbabilityVector();
|
||||
|
||||
final double mlEst = -10.0*Math.log10((double)mismatches/(double)(matches+mismatches));
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@
|
|||
|
||||
package org.broadinstitute.sting.gatk.walkers.indels;
|
||||
|
||||
import com.google.java.contract.Ensures;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.utils.Haplotype;
|
||||
import org.broadinstitute.sting.utils.MathUtils;
|
||||
|
|
@ -175,7 +176,8 @@ public class PairHMMIndelErrorModel {
|
|||
|
||||
}
|
||||
|
||||
public synchronized double[][] computeGeneralReadHaplotypeLikelihoods(final ReadBackedPileup pileup,
|
||||
@Ensures("result != null && result.length == pileup.getNumberOfElements()")
|
||||
public synchronized double[][] computeGeneralReadHaplotypeLikelihoods(final ReadBackedPileup pileup,
|
||||
final LinkedHashMap<Allele, Haplotype> haplotypeMap,
|
||||
final ReferenceContext ref,
|
||||
final int eventLength,
|
||||
|
|
|
|||
|
|
@ -90,7 +90,7 @@ public class ArtificialReadPileupTestProvider {
|
|||
return sampleNames;
|
||||
}
|
||||
public byte getRefByte() {
|
||||
return refBases.substring(offset,offset+1).getBytes()[0];
|
||||
return referenceContext.getBase();
|
||||
}
|
||||
|
||||
public ReferenceContext getReferenceContext() { return referenceContext;}
|
||||
|
|
@ -107,7 +107,7 @@ public class ArtificialReadPileupTestProvider {
|
|||
ArrayList<Allele> vcAlleles = new ArrayList<Allele>();
|
||||
Allele refAllele, altAllele;
|
||||
if (eventLength == 0) {// SNP case
|
||||
refAllele =Allele.create(refBases.substring(offset,offset+1),true);
|
||||
refAllele =Allele.create(referenceContext.getBase(),true);
|
||||
altAllele = Allele.create(altBases.substring(0,1), false);
|
||||
|
||||
} else if (eventLength>0){
|
||||
|
|
|
|||
Loading…
Reference in New Issue