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

Turning on allele trimming for the haplotype caller.

This commit is contained in:
Ryan Poplin 2012-10-10 10:47:26 -04:00
parent b543bddbb7
commit 2a9ee89c19
5 changed files with 23 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -283,7 +283,7 @@ public class GenotypingEngine {
final VariantContext mergedVC = VariantContextUtils.simpleMerge(genomeLocParser, eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
if( mergedVC == null ) { continue; }
final HashMap<Allele, ArrayList<Haplotype>> alleleHashMap = new HashMap<Allele, ArrayList<Haplotype>>();
HashMap<Allele, ArrayList<Haplotype>> alleleHashMap = new HashMap<Allele, ArrayList<Haplotype>>();
int aCount = 0;
for( final Allele a : mergedVC.getAlleles() ) {
alleleHashMap.put(a, alleleMapper.get(aCount++)); // BUGBUG: needs to be cleaned up and merged with alleleMapper
@ -308,9 +308,20 @@ public class GenotypingEngine {
}
genotypes.add( new GenotypeBuilder(sample).alleles(noCall).PL(genotypeLikelihoods).make() );
}
final VariantCallContext call = UG_engine.calculateGenotypes(new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), UG_engine.getUAC().GLmodel);
VariantContext call = UG_engine.calculateGenotypes(new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), UG_engine.getUAC().GLmodel);
if( call != null ) {
if( call.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!
final VariantContext vcCallTrim = VariantContextUtils.reverseTrimAlleles(call);
// also, need to update the allele -> haplotype mapping
final HashMap<Allele, ArrayList<Haplotype>> alleleHashMapTrim = new HashMap<Allele, ArrayList<Haplotype>>();
for( int iii = 0; iii < vcCallTrim.getAlleles().size(); iii++ ) { // BUGBUG: this is assuming that the original and trimmed alleles maintain the same ordering in the VC
alleleHashMapTrim.put(vcCallTrim.getAlleles().get(iii), alleleHashMap.get(call.getAlleles().get(iii)));
}
call = vcCallTrim;
alleleHashMap = alleleHashMapTrim;
}
returnCalls.add( new Pair<VariantContext, HashMap<Allele,ArrayList<Haplotype>>>(call, alleleHashMap) );
}
}

11
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
View File

@ -40,7 +40,6 @@ import java.util.*;
public class LikelihoodCalculationEngine {
private static final double LOG_ONE_HALF = -Math.log10(2.0);
private static final double BEST_LIKELIHOOD_THRESHOLD = 0.1;
private final byte constantGCP;
private final boolean DEBUG;
private final PairHMM pairHMM;
@ -184,7 +183,7 @@ public class LikelihoodCalculationEngine {
haplotypeLikelihood += readCounts_iii[kkk] * ( MathUtils.approximateLog10SumLog10(readLikelihoods_iii[kkk], readLikelihoods_jjj[kkk]) + LOG_ONE_HALF );
}
}
haplotypeLikelihoodMatrix[iii][jjj] = Math.max(haplotypeLikelihoodMatrix[iii][jjj], haplotypeLikelihood); // MathUtils.approximateLog10SumLog10(haplotypeLikelihoodMatrix[iii][jjj], haplotypeLikelihood); // BUGBUG: max or sum?
haplotypeLikelihoodMatrix[iii][jjj] = Math.max(haplotypeLikelihoodMatrix[iii][jjj], haplotypeLikelihood);
}
}
}
@ -323,11 +322,13 @@ public class LikelihoodCalculationEngine {
return bestHaplotypes;
}
public static Map<String, PerReadAlleleLikelihoodMap> partitionReadsBasedOnLikelihoods( final GenomeLocParser parser, final HashMap<String, ArrayList<GATKSAMRecord>> perSampleReadList, final HashMap<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList, final Pair<VariantContext, HashMap<Allele,ArrayList<Haplotype>>> call) {
public static Map<String, PerReadAlleleLikelihoodMap> partitionReadsBasedOnLikelihoods( final GenomeLocParser parser,
final HashMap<String, ArrayList<GATKSAMRecord>> perSampleReadList,
final HashMap<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList,
final Pair<VariantContext, HashMap<Allele,ArrayList<Haplotype>>> call) {
final Map<String, PerReadAlleleLikelihoodMap> returnMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
final GenomeLoc callLoc = parser.createGenomeLoc(call.getFirst());
for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
//final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>();
final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
final ArrayList<GATKSAMRecord> readsForThisSample = sample.getValue();
@ -352,7 +353,7 @@ public class LikelihoodCalculationEngine {
// only count the read if it overlaps the event, otherwise it is not added to the output read list at all
if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) {
for( final Allele a : call.getFirst().getAlleles() )
likelihoodMap.add(read,a,0.0);
likelihoodMap.add(read, a, 0.0);
}
}

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(CEUTRIO_BAM, "", "f5a809e3fbd9998f79b75bb2973209e1");
HCTestComplexVariants(CEUTRIO_BAM, "", "966da0de8466d21d79f1523488dff6bd");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -508,10 +508,10 @@ public class UnifiedGenotyperEngine {
// if we are subsetting alleles (either because there were too many or because some were not polymorphic)
// then we may need to trim the alleles (because the original VariantContext may have had to pad at the end).
if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext )
if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // limitedContext callers need to handle allele trimming on their own to keep their perReadAlleleLikelihoodMap alleles in sync
vcCall = VariantContextUtils.reverseTrimAlleles(vcCall);
if ( annotationEngine != null && !limitedContext ) {
if ( annotationEngine != null && !limitedContext ) { // limitedContext callers need to handle annotations on their own by calling their own annotationEngine
// Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
final ReadBackedPileup pileup = rawContext.getBasePileup();
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);

3
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -1340,10 +1340,7 @@ public class VariantContextUtils {
public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) {
// TODO - this function doesn't work with mixed records or records that started as mixed and then became non-mixed
// see whether we need to trim common reference base from all alleles
final int trimExtent = computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, false);
if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 )
return inputVC;