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Merge pull request #124 from broadinstitute/md_hc_lowmapq_read_filter 

HC now by default only uses reads with MAPQ >= 20 for assembly and calli...
This commit is contained in:
Ryan Poplin 2013-03-21 12:00:28 -07:00
parent b30deda7ee 7ae15dadbe
commit c15453542e
4 changed files with 55 additions and 11 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -56,7 +56,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.downsampling.DownsamplingUtils;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.filters.*;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -134,9 +134,9 @@ import java.util.*;
@PartitionBy(PartitionType.LOCUS)
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ActiveRegionTraversalParameters(extension=85, maxRegion=300)
@ReadFilters({HCMappingQualityFilter.class})
@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=250)
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
/**
* A raw, unfiltered, highly sensitive callset in VCF format.
*/

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
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@ -63,7 +63,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "91f4880910e436bf5aca0abbebd58948");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6dd29d6fec056419ab0fa03a7d43d85e");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -87,12 +87,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"f2add041ba1692db576ae9763a14b8a6");
"84616464aed68f4d9bc9e08472eff9c0");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"383320e81a1a3bee880fcc6cd0564452");
"e2d1023b846bfac31b4f7a3a4b90d931");
}
}

12
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -69,12 +69,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "75dbef605b28f02616b13bb5d8bf2fbd");
HCTest(CEUTRIO_BAM, "", "9859b136d05085b5ec0833035289106a");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "fa8705a5d3ada66470019fa7ddcb9b2c");
HCTest(NA12878_BAM, "", "27f660bf1c9a6ed7167d77022d401b73");
}
@Test(enabled = false) // can't annotate the rsID's yet
@ -85,7 +85,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@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",
"d41a886f69a67e01af2ba1a6b4a681d9");
"e25fc2196401a16347e0c730dbcbe828");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3a38f6fade253577d205a00db3e67828");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "325d7d73e0bd86b6cb146b249eda959a");
}
@Test
@ -111,14 +111,14 @@ 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("1e7b1bda6be5d3835ae318f2977cfbdd"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a"));
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("b6d63f558259883262ea84f339acb767"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ec97a0a65890169358842e765ff8dd15"));
executeTest("HCTestStructuralIndels: ", spec);
}

44
public/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java 100644
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@ -0,0 +1,44 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
/**
* Filter out reads with low mapping qualities.
*
* @author mdepristo
*/
public class HCMappingQualityFilter extends ReadFilter {
@Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for analysis with the HaplotypeCaller", required = false)
public int MIN_MAPPING_QUALTY_SCORE = 20;
public boolean filterOut(SAMRecord rec) {
return (rec.getMappingQuality() < MIN_MAPPING_QUALTY_SCORE);
}
}