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

Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs.

This commit is contained in:
Takuto Sato 2016-08-25 13:20:13 -04:00
parent 4aede99697
commit bc3b3ac0ec
2 changed files with 70 additions and 42 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

106
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/SomaticGenotypingEngine.java
View File

@ -107,8 +107,9 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
this.tumorSampleName = tumorSampleName;
this.matchedNormalSampleName = matchedNormalSampleName;
this.DEBUG_READ_NAME = DEBUG_READ_NAME;
// coverage related initialization
final double errorProbability = Math.pow(10, -(MTAC.POWER_CONSTANT_QSCORE/10));
final double errorProbability = Math.pow(10, -MTAC.POWER_CONSTANT_QSCORE / 10);
strandArtifactPowerCalculator = new TumorPowerCalculator(errorProbability, MTAC.STRAND_ARTIFACT_LOD_THRESHOLD, 0.0f);
}
@ -148,8 +149,12 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
if (activeRegionWindow == null ) throw new IllegalArgumentException("activeRegionWindow must be non-null, got "+activeRegionWindow);
if (activeAllelesToGenotype == null ) throw new IllegalArgumentException("activeAllelesToGenotype must be non-null, got "+activeAllelesToGenotype);
// Somatic Tumor/Normal Sample Handling
verifySamplePresence(tumorSampleName, readLikelihoods.samples());
if (!readLikelihoods.samples().contains(tumorSampleName)) {
throw new IllegalArgumentException("readLikelihoods does not contain the tumor sample "+ tumorSampleName);
}
// if we don't have the normal sample, we are in tumor only mode
// TODO: check in MuTect2.java for code we can skip when in tumor only mode
final boolean hasNormal = matchedNormalSampleName != null;
// update the haplotypes so we're ready to call, getting the ordered list of positions on the reference
@ -164,6 +169,7 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
if( loc < activeRegionWindow.getStart() || loc > activeRegionWindow.getStop() ) {
continue;
}
final List<VariantContext> eventsAtThisLoc = getVCsAtThisLocation(haplotypes, loc, activeAllelesToGenotype);
if( eventsAtThisLoc.isEmpty() ) { continue; }
@ -171,28 +177,46 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
// Create the event mapping object which maps the original haplotype events to the events present at just this locus
final Map<Event, List<Haplotype>> eventMapper = createEventMapper(loc, eventsAtThisLoc, haplotypes);
// TODO: priorityList is not sorted by priority, might as well just use eventsAtThisLoc.map(VariantContext::getSource)
final List<String> priorityList = makePriorityList(eventsAtThisLoc);
// merge variant contexts from multiple haplotypes into one variant context
// TODO: we should use haplotypes if possible, but that may have to wait for GATK4
VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList,
GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
if( mergedVC == null ) { continue; }
// TODO: this varaible needs a descriptive name
final Map<VariantContext, Allele> mergeMap = new LinkedHashMap<>();
mergeMap.put(null, mergedVC.getReference()); // the reference event (null) --> the reference allele
for(int iii = 0; iii < eventsAtThisLoc.size(); iii++) {
mergeMap.put(eventsAtThisLoc.get(iii), mergedVC.getAlternateAllele(iii)); // BUGBUG: This is assuming that the order of alleles is the same as the priority list given to simpleMerge function
for(int i = 0; i < eventsAtThisLoc.size(); i++) {
// TODO: as noted below, this operation seems dangerous. Understand how things can go wrong.
mergeMap.put(eventsAtThisLoc.get(i), mergedVC.getAlternateAllele(i)); // BUGBUG: This is assuming that the order of alleles is the same as the priority list given to simpleMerge function
}
/** TODO: the code in the for loop up to here needs refactor. The goal, as far as I can tell, is to create two things: alleleMapper and mergedVC
* alleleMapper maps alleles to haplotypes, and we need this to create readAlleleLikelihoods.
* To make alleleMapper we make mergeMap (of type VC -> Allele) and eventMapper (of type Event -> List(Haplotypes), where Event is essentialy Variant Context)
* If we just want a map of Alleles to Haplotypes, we should be able to do so directly; no need for intermediate maps, which just complicates the code.
**/
final Map<Allele, List<Haplotype>> alleleMapper = createAlleleMapper(mergeMap, eventMapper);
// converting ReadLikelihoods<Haplotype> to ReadLikeliHoods<Allele>
ReadLikelihoods<Allele> readAlleleLikelihoods = readLikelihoods.marginalize(alleleMapper, genomeLocParser.createPaddedGenomeLoc(genomeLocParser.createGenomeLoc(mergedVC), ALLELE_EXTENSION));
//LDG: do we want to do this before or after pulling out overlapping reads?
if (MTAC.isSampleContaminationPresent())
// LDG: do we want to do this before or after pulling out overlapping reads?
// TODO: do we want this at all? How does downsampling help?
if (MTAC.isSampleContaminationPresent()) {
readAlleleLikelihoods.contaminationDownsampling(MTAC.getSampleContamination());
}
// TODO: this is a good break point for a new method
// TODO: replace PRALM with ReadLikelihoods
final PerReadAlleleLikelihoodMap tumorPRALM = readAlleleLikelihoods.toPerReadAlleleLikelihoodMap(readAlleleLikelihoods.sampleIndex(tumorSampleName));
filterPRALMForOverlappingReads(tumorPRALM, mergedVC.getReference(), loc, false);
MuTect2.logReadInfo(DEBUG_READ_NAME, tumorPRALM.getLikelihoodReadMap().keySet(), "Present in Tumor PRALM after filtering for overlapping reads");
@ -208,11 +232,23 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
tumorLods.set(altAllele, tumorHetGenotypeLLs.get(altAllele) - tumorHetGenotypeLLs.getRef());
}
double INIT_NORMAL_LOD_THRESHOLD = -Double.MAX_VALUE;
double NORMAL_LOD_THRESHOLD = -Double.MAX_VALUE;
// TODO: another good breakpoint e.g. compute normal LOD/set thresholds
// TODO: anything related to normal should be encapsulated in Optional
// Normal LOD must exceed this threshold for the variant to make it in the vcf
// TODO: variable name too log
double normalLodThresholdForVCF = -Double.MIN_VALUE;
// A variant candidate whose normal LOD is below this threshold will be filtered as 'germline_risk'
// This is a more stringent threshold than normalLodThresholdForVCF
double normalLodFilterThreshold = -Double.MIN_VALUE;
PerReadAlleleLikelihoodMap normalPRALM = null;
final PerAlleleCollection<Double> normalLods = PerAlleleCollection.createPerAltAlleleCollection();
// TODO: this if statement should be a standalone method for computing normal LOD
// TODO: then we can do something like normalLodThreshold = hasNormal ? thisMethod() : Optional.empty()
// if normal bam is available, compute normal LOD
if (hasNormal) {
normalPRALM = readAlleleLikelihoods.toPerReadAlleleLikelihoodMap(readAlleleLikelihoods.sampleIndex(matchedNormalSampleName));
@ -222,13 +258,13 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
final GenomeLoc eventGenomeLoc = genomeLocParser.createGenomeLoc(activeRegionWindow.getContig(), loc);
final Collection<VariantContext> cosmicVC = tracker.getValues(MTAC.cosmicRod, eventGenomeLoc);
final Collection<VariantContext> dbsnpVC = tracker.getValues(MTAC.dbsnp.dbsnp, eventGenomeLoc);
// remove the effect of cosmic from dbSNP
final boolean germlineAtRisk = (!dbsnpVC.isEmpty() && cosmicVC.isEmpty());
INIT_NORMAL_LOD_THRESHOLD = MTAC.INITIAL_NORMAL_LOD_THRESHOLD; //only set this if this job has a normal
NORMAL_LOD_THRESHOLD = (germlineAtRisk)?MTAC.NORMAL_DBSNP_LOD_THRESHOLD:MTAC.NORMAL_LOD_THRESHOLD;
final boolean germlineAtRisk = !dbsnpVC.isEmpty() && cosmicVC.isEmpty();
// compute normal LOD = LL(X|REF)/LL(X|ALT) where ALT is the diploid HET with AF = 0.5
normalLodThresholdForVCF = MTAC.INITIAL_NORMAL_LOD_THRESHOLD;
normalLodFilterThreshold = germlineAtRisk ? MTAC.NORMAL_DBSNP_LOD_THRESHOLD : MTAC.NORMAL_LOD_THRESHOLD;
// compute normal LOD = LL(X|REF)/LL(X|ALT) where REF is the diploid HET with AF = 0.5
// note normal LOD is REF over ALT, the reciprocal of the tumor LOD
final PerAlleleCollection<Double> diploidHetAlleleFractions = PerAlleleCollection.createPerRefAndAltAlleleCollection();
for (final Allele allele : mergedVC.getAlternateAlleles()){
@ -246,40 +282,36 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
final Set<Allele> allelesThatPassThreshold = new HashSet<>();
Allele alleleWithHighestTumorLOD = null;
// TODO: use lambda
for (final Allele altAllele : mergedVC.getAlternateAlleles()) {
final boolean passesTumorLodThreshold = tumorLods.getAlt(altAllele) >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD;
final boolean passesNormalLodThreshold = hasNormal ? normalLods.getAlt(altAllele) >= INIT_NORMAL_LOD_THRESHOLD : true;
final boolean passesNormalLodThreshold = hasNormal ? normalLods.getAlt(altAllele) >= normalLodThresholdForVCF : true;
if (passesTumorLodThreshold && passesNormalLodThreshold) {
numPassingAlts++;
allelesThatPassThreshold.add(altAllele);
if (alleleWithHighestTumorLOD == null
|| tumorLods.getAlt(altAllele) > tumorLods.getAlt(alleleWithHighestTumorLOD)){
if (alleleWithHighestTumorLOD == null || tumorLods.getAlt(altAllele) > tumorLods.getAlt(alleleWithHighestTumorLOD)){
alleleWithHighestTumorLOD = altAllele;
}
}
}
if (numPassingAlts == 0) {
continue;
}
final VariantContextBuilder callVcb = new VariantContextBuilder(mergedVC);
// FIXME: can simply get first alternate since above we only deal with Bi-allelic sites...
final int haplotypeCount = alleleMapper.get(mergedVC.getAlternateAllele(0)).size();
final int haplotypeCount = alleleMapper.get(alleleWithHighestTumorLOD).size();
callVcb.attribute(GATKVCFConstants.HAPLOTYPE_COUNT_KEY, haplotypeCount);
callVcb.attribute(GATKVCFConstants.TUMOR_LOD_KEY, tumorLods.getAlt(alleleWithHighestTumorLOD));
if (hasNormal) {
callVcb.attribute(GATKVCFConstants.NORMAL_LOD_KEY, normalLods.getAlt(alleleWithHighestTumorLOD));
if (normalLods.getAlt(alleleWithHighestTumorLOD) < NORMAL_LOD_THRESHOLD) {
if (normalLods.getAlt(alleleWithHighestTumorLOD) < normalLodFilterThreshold) {
callVcb.filter(GATKVCFConstants.GERMLINE_RISK_FILTER_NAME);
}
}
// M1-style strand artifact filter
// TODO: this should be a separate method
// TODO: move code to MuTect2::calculateFilters()
// skip if VC has multiple alleles - it will get filtered later anyway
if (MTAC.ENABLE_STRAND_ARTIFACT_FILTER && numPassingAlts == 1) {
final PerReadAlleleLikelihoodMap forwardPRALM = new PerReadAlleleLikelihoodMap();
final PerReadAlleleLikelihoodMap reversePRALM = new PerReadAlleleLikelihoodMap();
@ -304,12 +336,10 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
final double tumorSBpower_fwd = strandArtifactPowerCalculator.cachedPowerCalculation(forwardPRALM.getNumberOfStoredElements(), altAlleleFractions.getAlt(alleleWithHighestTumorLOD));
final double tumorSBpower_rev = strandArtifactPowerCalculator.cachedPowerCalculation(reversePRALM.getNumberOfStoredElements(), altAlleleFractions.getAlt(alleleWithHighestTumorLOD));
callVcb.attribute(GATKVCFConstants.TLOD_FWD_KEY, tumorLod_fwd);
callVcb.attribute(GATKVCFConstants.TLOD_REV_KEY, tumorLod_rev);
callVcb.attribute(GATKVCFConstants.TUMOR_SB_POWER_FWD_KEY, tumorSBpower_fwd);
callVcb.attribute(GATKVCFConstants.TUMOR_SB_POWER_REV_KEY, tumorSBpower_rev);
// TODO: add vcf INFO fields. see callVcb.attribute(GATKVCFConstants.HAPLOTYPE_COUNT_KEY, haplotypeCount);
if ((tumorSBpower_fwd > MTAC.STRAND_ARTIFACT_POWER_THRESHOLD && tumorLod_fwd < MTAC.STRAND_ARTIFACT_LOD_THRESHOLD) ||
(tumorSBpower_rev > MTAC.STRAND_ARTIFACT_POWER_THRESHOLD && tumorLod_rev < MTAC.STRAND_ARTIFACT_LOD_THRESHOLD))
@ -323,9 +353,15 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
// build genotypes TODO: this part needs review and refactor
final List<Allele> tumorAlleles = Arrays.asList(mergedVC.getReference(), alleleWithHighestTumorLOD);
// TODO: estimateAlleleFraction should not repeat counting allele depths
final PerAlleleCollection<Integer> tumorAlleleDepths = getRefAltCount(mergedVC, tumorPRALM, false);
final int tumorRefAlleleDepth = tumorAlleleDepths.getRef();
final int tumorAltAlleleDepth = tumorAlleleDepths.getAlt(alleleWithHighestTumorLOD);
final Genotype tumorGenotype = new GenotypeBuilder(tumorSampleName, tumorAlleles)
.AD(new int[] { tumorRefAlleleDepth, tumorAltAlleleDepth })
.attribute(GATKVCFConstants.ALLELE_FRACTION_KEY, altAlleleFractions.getAlt(alleleWithHighestTumorLOD))
.make(); // TODO: add ADs?
.make();
final List<Genotype> genotypes = new ArrayList<>();
genotypes.add(tumorGenotype);
@ -335,20 +371,18 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
// if we are calling with a normal, build the genotype for the sample to appear in vcf
if (hasNormal) {
final PerAlleleCollection<Integer> normalCounts = getRefAltCount(mergedVC, normalPRALM, false);
final int normalRefAlleleDepth = normalCounts.getRef();
final int normalAltAlleleDepth = normalCounts.getAlt(alleleWithHighestTumorLOD);
final int[] normalAlleleDepths = { normalRefAlleleDepth, normalAltAlleleDepth };
final PerAlleleCollection<Integer> normalAlleleDepths = getRefAltCount(mergedVC, normalPRALM, false);
final int normalRefAlleleDepth = normalAlleleDepths.getRef();
final int normalAltAlleleDepth = normalAlleleDepths.getAlt(alleleWithHighestTumorLOD);
final double normalAlleleFraction = (double) normalAltAlleleDepth / ( normalRefAlleleDepth + normalAltAlleleDepth);
final Genotype normalGenotype = new GenotypeBuilder(matchedNormalSampleName, homRefAllelesforNormalGenotype)
.AD(normalAlleleDepths)
.AD(new int[] { normalRefAlleleDepth, normalAltAlleleDepth })
.attribute(GATKVCFConstants.ALLELE_FRACTION_KEY, normalAlleleFraction)
.make();
genotypes.add(normalGenotype);
}
//only use alleles found in the tumor (
final VariantContext call = new VariantContextBuilder(callVcb).alleles(tumorAlleles).genotypes(genotypes).make();
// how should we be making use of _perSampleFilteredReadList_?
@ -371,12 +405,6 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
return new CalledHaplotypes(outputCalls, calledHaplotypes);
}
private void verifySamplePresence(final String sampleName, final List<String> samples) {
if (!samples.contains(sampleName)) {
throw new IllegalArgumentException("Unable to find sample name "+sampleName+"in sample list of " + StringUtil.join(",", samples));
}
}
/** Calculate the likelihoods of hom ref and each het genotype of the form ref/alt
*
* @param mergedVC input VC

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java
View File

@ -149,7 +149,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
*/
@Test
public void testFalsePositivesDream3() {
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "c23f794866797f9bbcb3ed04451758be"); // e2413f4166b6ed20be6cdee6616ba43d
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "c9eec57bbc93ea630c202b7620f8dca8"); // e2413f4166b6ed20be6cdee6616ba43d
}
/**
@ -170,12 +170,12 @@ public class MuTect2IntegrationTest extends WalkerTest {
@Test
public void testStrandArtifactFilter(){
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "--enable_strand_artifact_filter", "75c9349ff9f8dc84291396ac50871f64");
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "--enable_strand_artifact_filter", "1686c1a0e63768497f21b9d7bb6548c5");
}
@Test
public void testClusteredReadPositionFilter() {
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "--enable_clustered_read_position_filter", "c333f7dc11e39e0713147ad9af2bf4db");
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "--enable_clustered_read_position_filter", "b44c23af7de84f96d2371db25d29aba2");
}