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Raising per-sample limits on the number of reads in ART and HC. 

-- Active Region Traversal was using per sample limits on the number of reads that were too low, especially now that we are running one sample at a time. This caused issues with high confidence variants being dropped in high coverage data.
-- HaplotypeCallerGVCFIntegrationTest PL/annotation changes due to using more reads in those tests
-- Removed a CountReadsInActiveRegionsIntegrationTest test for excessive coverage because the read coverage no longer goes over the limits in ART
This commit is contained in:
Ryan Poplin 2015-01-07 11:32:28 -05:00
parent 03203e249e
commit 2e5f9db758
3 changed files with 18 additions and 19 deletions
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9
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -235,7 +235,7 @@ import java.util.*;
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ActiveRegionTraversalParameters(extension=100, maxRegion=300)
@ReadFilters({HCMappingQualityFilter.class})
@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=250)
@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=500)
public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, Integer> implements AnnotatorCompatible, NanoSchedulable {
// -----------------------------------------------------------------------------------------------
// general haplotype caller arguments
@ -696,10 +696,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
* not reducing coverage at any read start to less than minReadsPerAlignmentStart
*/
@Argument(fullName = "maxReadsInRegionPerSample", shortName = "maxReadsInRegionPerSample", doc="Maximum reads in an active region", required = false)
protected int maxReadsInRegionPerSample = 1000;
protected int maxReadsInRegionPerSample = 10000;
@Argument(fullName = "minReadsPerAlignmentStart", shortName = "minReadsPerAlignStart", doc="Minimum number of reads sharing the same alignment start for each genomic location in an active region", required = false)
protected int minReadsPerAlignmentStart = 5;
protected int minReadsPerAlignmentStart = 10;
private byte MIN_TAIL_QUALITY;
private static final byte MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION = 6;
@ -1183,6 +1183,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
protected AssemblyResultSet assembleReads(final ActiveRegion activeRegion, final List<VariantContext> giveAlleles) {
// Create the reference haplotype which is the bases from the reference that make up the active region
finalizeActiveRegion(activeRegion); // handle overlapping fragments, clip adapter and low qual tails
if( SCAC.DEBUG ) { logger.info("Assembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads: (with overlap region = " + activeRegion.getExtendedLoc() + ")"); }
final byte[] fullReferenceWithPadding = activeRegion.getActiveRegionReference(referenceReader, REFERENCE_PADDING);
final GenomeLoc paddedReferenceLoc = getPaddedLoc(activeRegion);
@ -1301,8 +1302,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
private void finalizeActiveRegion( final ActiveRegion activeRegion ) {
if (activeRegion.isFinalized()) return;
if( SCAC.DEBUG ) { logger.info("Assembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads: (with overlap region = " + activeRegion.getExtendedLoc() + ")"); }
// Loop through the reads hard clipping the adaptor and low quality tails
final List<GATKSAMRecord> readsToUse = new ArrayList<>(activeRegion.getReads().size());
for( final GATKSAMRecord myRead : activeRegion.getReads() ) {

24
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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@ -77,9 +77,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "646ec07bd026da1e72b5e789f5aa3a3d"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cb598bee733db0461f6a24d265daed45"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c53ecb02a41511123dc4e1573dd516f6"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "c223d6fe112d2bb698811600c3b7f6af"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "dacb94af2632e4dc4a1948306dd1661c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "ef9093880efedac09b78c8fb26420e84"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "9dbe7721ebfba9aefcfbfd1bdd62f2c4"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "4c99694b14beffd694f9738697b8f9d5"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "87d1e673e2512aefdceddd0293e4f346"});
return tests.toArray(new Object[][]{});
}
@ -96,10 +96,10 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "83b96e3e364821c51e6a2c2a64616b24"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f38178834961798d79e7190dbca004bf"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a6db14e73e0a270b9d3e2035acfc1d2f"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "1c3570461e96ad6d66c6abb0fd6ee865"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2a5a7057faba3cd488e40186072156af"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "afede7dbbcbe0e1af4abba7fc7bef479"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "853bd2f47496b3e8d1fe85657e4bf812"});
final String NA12878bandedResolutionMD5 = "46bf5ca5142770a31fe0fbcd1fc988b4";
final String NA12878bandedResolutionMD5 = "87900cbed775471f1a7ad6582b0581f9";
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@ -119,9 +119,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "254b4bed7fc8ef5d3c4cb4ebf4ea73c2"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "3f9e2b721c3bc8a6d76aa75bb7544f28"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "bfd12d811446cde2466508033cae7122"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "eac793500fbc7de46259000dbbcdd27d"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "dc1b8abd195b75e147ac78fdbd4e2b65"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "124c794c78edfe74558307a203f93294"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "8e35def5c821afa9b6fbeed0aed0a866"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8cebba1996a2aca29370c4d85f12128c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "8abc60102776b34e22858ca157c784a9"});
return tests.toArray(new Object[][]{});
}
@ -137,9 +137,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "d8daf60c68f39875680cc037f264ccc0"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "dd1e6ee5e242fa1caa7f64a9605e4b16"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a040bb2ebacf5afab3490504730043a1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "8b44f98c12ed7949d716852e0a21b346"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "4872ba8a27a29c9cac5e5c787ca853b5"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "65fc0938ca7df792a36413465878bc89"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d5ed4c847250a1096b6a5a2eac61d8dc"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "0d41cee1d7bd3c6df9816cc87a8a9d7c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "f8775dd95c3b185fc6abdb3ef8da3833"});
return tests.toArray(new Object[][]{});
}

4
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java
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@ -85,7 +85,7 @@ public @interface ActiveRegionTraversalParameters {
* of coverage in the engine.
* @return the maximum number of reads we're willing to hold in memory
*/
public int maxReadsToHoldInMemoryPerSample() default 3000;
public int maxReadsToHoldInMemoryPerSample() default 30000;
/**
* No matter what the per sample value says, we will never hold more than this
@ -93,5 +93,5 @@ public @interface ActiveRegionTraversalParameters {
* of reads in the case where we have a lot of samples.
* @return the maximum number of reads to hold in memory
*/
public int maxReadsToHoldTotal() default 1000000;
public int maxReadsToHoldTotal() default 10000000;
}