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a) Bad bug fix to CombineVariants: when indels were being merged, the reference base provided was wrong - ref.getBases()[0] was being used, but this returns bease at start of window. Instead, the reference at current locus should be used. 

b) Cosmetic change to Beagle annotation description.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3861 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-07-23 15:13:47 +00:00
parent 4ff8b8fc0e
commit 5eef15cfdf
3 changed files with 11 additions and 10 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -113,15 +113,17 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
return 0;
// get all of the vcf rods at this locus
// Need to provide reference bases to simpleMerge starting at current locus
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, priority, variantMergeOption, genotypeMergeOption, true, printComplexMerges, ref.getBases(), SET_KEY);
VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, priority, variantMergeOption,
genotypeMergeOption, true, printComplexMerges, ref.getBasesAtLocus(1), SET_KEY);
//out.printf(" merged => %s%nannotated => %s%n", mergedVC, annotatedMergedVC);
if ( mergedVC != null ) { // only operate at the start of events
VariantContext annotatedMergedVC = engine.annotateContext(tracker, ref, mergedVC);
vcfWriter.add(annotatedMergedVC, ref.getBases());
vcfWriter.add(annotatedMergedVC, ref.getBasesAtLocus(1));
}
return vcs.isEmpty() ? 0 : 1;

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
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@ -95,9 +95,9 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
final RMDTrack rod = source.getReferenceOrderedData();
if (rod.getName().equals(COMP_ROD_NAME)) {
hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Hapmap at this site"));
hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Hapmap at this site"));
hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Hapmap at this site"));
hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Comparison ROD at this site"));
hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Comparison ROD at this site"));
hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Comparison ROD at this site"));
break;
}

9
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -59,14 +59,13 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "bbeb813ff559b630570725419e4e1adc"); }
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "38b7e64b91c726867a604cf95b9cb10a"); } // official project VCF files in tabix format
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "9f35f86f45e13819993d269f5a798854"); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "02f3627501e782a5d3dece1dc69e7dca"); }
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "4c667935099544a1863e70ae88ddd685"); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "cbd061cf35e0ffc48621111a602f3871"); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "f3fce9ae729548e7e7c378a8282df235"); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "c87851a23df6165225a964b68d240e05"); }
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f2a2854f26734c8c3412f842a245fd34"); }
// todo - Guillermo / Eric, please fix. createVariantContextWithPaddedAlleles() func itself or call in merge is broken.
//@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "d28282213298878fd315a24d533db122"); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "a66a799b1ae9fd09b40f78af6ef538d8"); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "a9126d1cbe1fdf741236763fb3e3461f"); }
}