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Changing the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.

This commit is contained in:
Ryan Poplin 2012-12-17 11:27:44 -05:00
parent 1d18ee26cc
commit 98f18b5f9e
3 changed files with 18 additions and 10 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -44,13 +44,15 @@ import java.util.*;
public class GenotypingEngine {
private final boolean DEBUG;
private final boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS;
private final static List<Allele> noCall = new ArrayList<Allele>(); // used to noCall all genotypes until the exact model is applied
private final static Allele SYMBOLIC_UNASSEMBLED_EVENT_ALLELE = Allele.create("<UNASSEMBLED_EVENT>", false);
private final VariantAnnotatorEngine annotationEngine;
public GenotypingEngine( final boolean DEBUG, final VariantAnnotatorEngine annotationEngine ) {
public GenotypingEngine( final boolean DEBUG, final VariantAnnotatorEngine annotationEngine, final boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ) {
this.DEBUG = DEBUG;
this.annotationEngine = annotationEngine;
this.USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = USE_FILTERED_READ_MAP_FOR_ANNOTATIONS;
noCall.add(Allele.NO_CALL);
}
@ -192,7 +194,9 @@ public class GenotypingEngine {
}
final VariantContext call = UG_engine.calculateGenotypes(new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), UG_engine.getUAC().GLmodel);
if( call != null ) {
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = filterToOnlyOverlappingReads( genomeLocParser, alleleReadMap, perSampleFilteredReadList, call );
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap_annotations = ( USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ? alleleReadMap :
convertHaplotypeReadMapToAlleleReadMap( haplotypeReadMap, alleleMapper, 0.0, UG_engine.getUAC().contaminationLog ) );
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = filterToOnlyOverlappingReads( genomeLocParser, alleleReadMap_annotations, perSampleFilteredReadList, call );
VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, call);
if( annotatedCall.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!

6
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -142,6 +142,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "If specified, use additional trigger on variants found in an external alleles file", required=false)
protected boolean USE_ALLELES_TRIGGER = false;
@Advanced
@Argument(fullName="useFilteredReadsForAnnotations", shortName="useFilteredReadsForAnnotations", doc = "If specified, use the contamination-filtered read maps for the purposes of annotating variants", required=false)
protected boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = false;
/**
* rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
* dbSNP is not used in any way for the calculations themselves.
@ -280,7 +284,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
assemblyEngine = new SimpleDeBruijnAssembler( DEBUG, graphWriter );
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine );
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS );
}
//---------------------------------------------------------------------------------------------------------------

14
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -21,19 +21,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "d602d40852ad6d2d094be07e60cf95bd");
HCTest(CEUTRIO_BAM, "", "b8866e674c0f1ea9338f29a7ebe65207");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "70ad9d53dda4d302b879ca2b7dd5b368");
HCTest(NA12878_BAM, "", "6f371736b36d99913764e8eecd4394a5");
}
// TODO -- add more tests for GGA mode, especially with input alleles that are complex variants and/or not trimmed
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"fe84caa79f59ecbd98fcbcd5b30ab164");
"eef673f79144fab1033c6e286e7c0af3");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -55,7 +55,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "338ab3b7dc3d54df8af94c0811028a75");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "0761ff5cbf279be467833fa6708bf360");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -72,14 +72,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("2f4ed6dc969bee041215944a9b24328f"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("f9881d61694659b2fdc4c092d20d48b6"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("d8d6f2ebe79bca81c8a0911daa153b89"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3f589ef62793ac452bbcc99a77488657"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -93,7 +93,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("d01cb5f77ed5aca1d228cfbce9364c21"));
Arrays.asList("4c5ab9e677a0aed6a430055989e27888"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
}