From 8b29030467b0e5e4459d1686a98d17937fc841f1 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Mon, 25 Feb 2013 15:38:29 -0500 Subject: [PATCH] Change default downsampling coverage target for the HaplotypeCaller to 250 -was previously set to 30, which seems far too aggressive given that with ActiveRegionWalkers, as with LocusWalkers, this limits the depth of any pileup returned by LIBS -250 is a more conservative default used by the UG -can adjust down/up later based on further experiments (GSA-699 will remain open) -verified with Ryan that all integration test differences are either innocent or represent an improvement GSA-699 --- .../haplotypecaller/HaplotypeCaller.java | 2 +- .../BiasedDownsamplingIntegrationTest.java | 8 ++++---- .../HaplotypeCallerIntegrationTest.java | 18 +++++++++--------- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 30749a820..64c762e97 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -133,7 +133,7 @@ import java.util.*; @PartitionBy(PartitionType.LOCUS) @BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN) @ActiveRegionTraversalParameters(extension=85, maxRegion=300) -@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=30) +@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=250) public class HaplotypeCaller extends ActiveRegionWalker implements AnnotatorCompatible { /** diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java index 08428b5aa..3f2ace800 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java @@ -255,7 +255,7 @@ public class BiasedDownsamplingIntegrationTest extends WalkerTest { final String baseCommand = "-T HaplotypeCaller -R " + b36KGReference + " --no_cmdline_in_header --dbsnp " + b36dbSNP129; WalkerTestSpec spec = new WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -contamination 0.20", 1, - Arrays.asList("3a66513cdfef46f315d5ada8a104822f")); + Arrays.asList("c3a253467ead7b1cfe9fd9dd310828b1")); executeTest("HC calling with contamination_percentage_to_filter 0.20", spec); } @@ -283,17 +283,17 @@ public class BiasedDownsamplingIntegrationTest extends WalkerTest { @Test public void testHCFlatContaminationCase1() { - testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "9dbd17769e091ce759efda050cd4f8b2"); + testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "c3e695381d8627e3922d8c642b66c3ce"); } @Test public void testHCFlatContaminationCase2() { - testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "b8cee98c9c693fd336fc5e574dd744ed"); + testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "002d2b45336d88d7c04e19f9f26e29d9"); } @Test public void testHCFlatContaminationCase3() { - testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "e7309bd594b8e4b54b712f9877518b8e"); + testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "1809a33ac112d1a3bd7a071c566794dd"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 05a7ce3be..856ef58a1 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -68,12 +68,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "a9748a39604c4ec8bbdb2cb809a971f1"); + HCTest(CEUTRIO_BAM, "", "aac5517a0a64ad291b6b00825d982f7f"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "c55ebed976767e1f93d2e8ada9d52bf8"); + HCTest(NA12878_BAM, "", "3bfab723fb0f3a65998d82152b67ed15"); } @Test(enabled = false) @@ -84,7 +84,7 @@ 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", - "70a53e566e6a7090e2f29ed608e9d84f"); + "283524b3e3397634d4cf0dc2b8723002"); } private void HCTestComplexGGA(String bam, String args, String md5) { @@ -96,13 +96,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "1d9cd5017e420d5862b7b94e6cb5de3b"); + "417174e043dbb8b86cc3871da9b50536"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "10fdbfeb3b4ea1af7f242a8aca83cb9b"); + "f2df7a8f53ce449e4a8e8f8496e7c745"); } private void HCTestComplexVariants(String bam, String args, String md5) { @@ -125,7 +125,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { // TODO -- need a better symbolic allele test @Test public void testHaplotypeCallerSingleSampleSymbolic() { - HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "f893aa7afef71705df7f040b22440a2d"); + HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "56f2ef9acc6c0d267cf2b7a447d87fb7"); } private void HCTestIndelQualityScores(String bam, String args, String md5) { @@ -146,7 +146,7 @@ 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("0689d2c202849fd05617648eaf429b9a")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ccd30e226f097a40cdeebaa035a290a7")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @@ -175,7 +175,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, - Arrays.asList("2ab038f4f6c262b3245b6fa549659c5e")); + Arrays.asList("adb08cb25e902cfe0129404a682b2169")); executeTest("HC calling on a ReducedRead BAM", spec); } @@ -183,7 +183,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testReducedBamWithReadsNotFullySpanningDeletion() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1, - Arrays.asList("56fc9110974bfa9c9fe196b0d4af4e64")); + Arrays.asList("6debe567cd5ed7eb5756b6605a151f56")); executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); } }