From 5695f22da8740eb7edc6489f4569773a51c2c804 Mon Sep 17 00:00:00 2001 From: Tim Fennell Date: Thu, 7 Aug 2014 10:43:09 -0400 Subject: [PATCH] Changed the default GVCF Q Bands from 5,20,60 to be 1..60 by 1s, 60...90 by 10s and 99 in order to give finer resolution for homref PLs and ADs at lower confidences and somewhat higher resolution at higher confidences. --- .../tools/walkers/haplotypecaller/HaplotypeCaller.java | 5 ++++- .../HaplotypeCallerGVCFIntegrationTest.java | 8 ++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index 6a4222c09..cfb29d272 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -408,7 +408,10 @@ public class HaplotypeCaller extends ActiveRegionWalker, In */ @Advanced @Argument(fullName="GVCFGQBands", shortName="GQB", doc="Emit experimental reference confidence scores", required = false) - protected List GVCFGQBands = Arrays.asList(5, 20, 60); + protected List GVCFGQBands = new ArrayList(70) {{ + for (int i=1; i<=60; ++i) add(i); + add(70); add(80); add(90); add(99); + }}; /** * This parameter determines the maximum size of an indel considered as potentially segregating in the diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index 89b68114f..fca9b91fb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -69,10 +69,10 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { // this functionality can be adapted to provide input data for whatever you might want in your data tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "9db87ae56df22456f3c08024384f3e5e"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "4a006f9e39cacc3ae84384ad56ca22a2"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb048cbfa5cc058d680f9be5fd689767"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fe014592c9fa8d442508a96eb09e0c93"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d5c07fa3edca496a84fd17cecad06230"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "330685c734e277d70a44637de85ad54d"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e6ec90da053a612f0c615e221eb34baa"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "b01a2c222a3f00a675f5534c3b449919"}); return tests.toArray(new Object[][]{}); } @@ -137,7 +137,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testWrongGVCFNonVariantRecordOrderBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9fecd24420579f321157e5605b6cd7f2")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("d595dae0e3f993047c22c6e520e190aa")); spec.disableShadowBCF(); executeTest("testMissingGVCFIndexingStrategyException", spec); } @@ -149,7 +149,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testNoCallGVCFMissingPLsBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("95bae0b4a8fe9bfcf71762704b22a76e")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("2a91768430a84dbae8d40242dee8c9b8")); spec.disableShadowBCF(); executeTest("testNoCallGVCFMissingPLsBugFix", spec); }