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

Adding LowQual filter to the output of the HaplotypeCaller.

This commit is contained in:
Ryan Poplin 2012-08-10 11:25:14 -04:00
parent 67d4148b32
commit 5f82ffd5d8
2 changed files with 8 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -275,6 +275,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
headerInfo.add(new VCFInfoHeaderLine("extType", 1, VCFHeaderLineType.String, "Extended type of event: SNP, MNP, INDEL, or COMPLEX"));
headerInfo.add(new VCFInfoHeaderLine("QDE", 1, VCFHeaderLineType.Float, "QD value divided by the number of variants found on the haplotype that contained this variant"));
// FILTER fields are added unconditionally as it's not always 100% certain the circumstances
// where the filters are used. For example, in emitting all sites the lowQual field is used
headerInfo.add(new VCFFilterHeaderLine(UnifiedGenotyperEngine.LOW_QUAL_FILTER_NAME, "Low quality"));
vcfWriter.writeHeader(new VCFHeader(headerInfo, samples));
try {

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -20,17 +20,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "7b4e76934e0c911220b4e7da8776ab2b");
HCTest(CEUTRIO_BAM, "", "882ece8391cfec30ab658970a487d078");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "fcf0cea98a571d5e2d1dfa8b5edc599d");
HCTest(NA12878_BAM, "", "6f458e04251bc4c09b5b544d46f19d68");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "ff370c42c8b09a29f1aeff5ac57c7ea6");
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "c172791007f867bf3b975d4194564d9e");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -41,7 +41,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(CEUTRIO_BAM, "", "6f9fda3ea82c5696bed1d48ee90cd76b");
HCTestComplexVariants(CEUTRIO_BAM, "", "94186811016b332a58c150df556278f8");
}
}