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Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.

This commit is contained in:
Samuel Lee 2015-09-23 14:31:16 -04:00
parent aadf6645f6
commit 0dacf60012
4 changed files with 16 additions and 5 deletions
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4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
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@ -382,8 +382,8 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
final int ploidy = oldGT.getPloidy();
final List<Allele> refAlleles = Collections.nCopies(ploidy,VC.getReference());
//keep 0 depth samples as no-call
if (depth > 0) {
//keep 0 depth samples and 0 GQ samples as no-call
if (depth > 0 && oldGT.hasGQ() && oldGT.getGQ() > 0) {
builder.alleles(refAlleles);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
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@ -229,7 +229,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
// Just checking that this does not fail, hence no output files and MD5
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants --no_cmdline_in_header -o %s "
+ " -R " + hg19RefereneWithChrPrefixInChromosomeNames
+ " -R " + hg19ReferenceWithChrPrefixInChromosomeNames
+ " -V " + privateTestDir + "WES-chr1.DEL.vcf"
+ " -V " + privateTestDir + "WGS-chr1.DEL.vcf"
+ " -genotypeMergeOptions UNIQUIFY",

13
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
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@ -145,7 +145,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
1,
Arrays.asList("92513f9a6f34829ef455a379e87e09cd"));
Arrays.asList("13c24e54c17e667a9647066aed54da76"));
executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
}
@ -549,4 +549,15 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
spec.disableShadowBCF();
executeTest("testSACMultisampleTetraploid", spec);
}
@Test(enabled = true)
public void testSetZeroRGQsToNoCall() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" +
" -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" +
" -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames),
1,
Arrays.asList("2daf1956e9d4d5f522fa953c6b4a23a4"));
executeTest("testSetZeroRGQsToNoCall", spec);
}
}

2
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
View File

@ -98,7 +98,7 @@ public abstract class BaseTest {
public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
public static final String b37KGReferenceWithDecoy = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta";
public static final String hg19RefereneWithChrPrefixInChromosomeNames = "/humgen/gsa-hpprojects/GATK/bundle/current/hg19/ucsc.hg19.fasta";
public static final String hg19ReferenceWithChrPrefixInChromosomeNames = "/humgen/gsa-hpprojects/GATK/bundle/current/hg19/ucsc.hg19.fasta";
public static final String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
public static final String validationDataLocation = GATKDataLocation + "Validation_Data/";
public static final String evaluationDataLocation = GATKDataLocation + "Evaluation_Data/";