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Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10

This commit is contained in:
Ron Levine 2016-11-10 16:53:13 -05:00
parent 94fe2aabbd
commit bcbd7fe952
10 changed files with 37 additions and 37 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java
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@ -122,7 +122,7 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{
* is the default).
*/
@Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false)
public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
public double STANDARD_CONFIDENCE_FOR_CALLING = 10.0;
/**
* This argument allows you to emit low quality calls as filtered records.

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
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@ -378,7 +378,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
// we want to keep the NON_REF symbolic allele but only in the absence of a non-symbolic allele, e.g.
// if we combined a ref / NON_REF gVCF with a ref / alt gVCF
final boolean isNonRefWhichIsLoneAltAllele = alternativeAlleleCount == 1 && allele.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
final boolean isPlausible = afcr.isPolymorphicPhredScaledQual(allele, configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING/3);
final boolean isPlausible = afcr.isPolymorphicPhredScaledQual(allele, configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING);
siteIsMonomorphic &= !isPlausible;
boolean toOutput = (isPlausible || forceKeepAllele(allele) || isNonRefWhichIsLoneAltAllele);
@ -793,7 +793,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
final double normalizedLog10ACeq0Posterior = log10ACeq0Posterior - log10PosteriorNormalizationConstant;
// This is another condition to return a 0.0 also present in AFCalculator code as well.
if (normalizedLog10ACeq0Posterior >= QualityUtils.qualToErrorProbLog10(configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING/3))
if (normalizedLog10ACeq0Posterior >= QualityUtils.qualToErrorProbLog10(configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING))
return 0.0;
return 1.0 - Math.pow(10.0, normalizedLog10ACeq0Posterior);

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java
View File

@ -70,7 +70,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
for ( final int nt : Arrays.asList(1, 2) )
for ( final int nct : Arrays.asList(1, 2) ) {
tests.add(new Object[]{ "BOTH", "52f590f6b37a1b3b12042ae917738965", nt, nct });
tests.add(new Object[]{ "BOTH", "e2fdd36a4eda18f748df944b428fa392", nt, nct });
}
return tests.toArray(new Object[][]{});

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
View File

@ -69,7 +69,7 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testSNP_ACS_Pools() {
executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "ebdf749d404aaef298780a53059a4f93");
executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "853b47780322b8133577aea528b9fd77");
}
@Test(enabled = true)
@ -88,6 +88,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
//TODO the old MD5 is kept for the record.
//TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach.
// executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "5b76f96b6b74944e0c0d9914700588f0");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "f6b9e1ac0c51c9702525ee52bb2db18a");
}
}

12
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
View File

@ -78,7 +78,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("32bece91e170d623092817738faddb4e"));
Arrays.asList("96afa04944156c1ca5028e5506ba8b94"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -105,7 +105,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("dd66e5f8a6e43be0e473251185a4f38a"));
Arrays.asList("7e211573190003342af274e64a0612fb"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -115,7 +115,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("aa56ed44e77162efce45c936c485769e"));
Arrays.asList("50622e495cad2a24fbc4a80f1281d4dc"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -125,7 +125,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("a4b6434c59c4b119e480ddafc86de234"));
Arrays.asList("50622e495cad2a24fbc4a80f1281d4dc"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -181,7 +181,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("2a82d1586b2148e8d902da5cf8538210"));
Arrays.asList("0d1a5c865c382f1f0ca6f0f104478366"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -189,7 +189,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("3184a3f58b3aeafcd97280af708a04bb"));
Arrays.asList("aab86cec61adaeb3a5c6887e70211663"));
executeTest("test minIndelFraction 0.25", spec);
}

16
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -129,12 +129,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f6937cc8ec068f2d38b5d277a92be34b");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "06386b0a4495583aa924e5addd56c5dc");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "1cddd7b1e730765c2b7b55d8a1d69b4c");
testOutputParameters("--output_mode EMIT_ALL_SITES", "b8b21ad6a2ff1f908e8e0073b57ba0e0");
}
private void testOutputParameters(final String args, final String md5) {
@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "6b8bdde9d303139806c5177fae53b1fd" );
testHeterozosity( 0.01, "7bbba110f720fc8c115fe2d53b34d693" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "b1604d1ba68dfe2fcfb861ef6420a8ba" );
testHeterozosity( 1.0 / 1850, "767e8eacd216ac7437456e690287cecf" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -238,7 +238,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "398d3ad38834fea8961ab6f46a21dc4b";
String md5 = "75b4b097747f91b8b7ceea153d2b7e1c";
final String myCommand = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("7ed55f70feeacf8ecc6b36f0d741dfc7"));
Arrays.asList("6464138c0bd2ab2cac06773f19e37a4c"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("90224ac1c9e2ce9b77fee8dd6e044efe"));
Arrays.asList("8885492069487efcf67e13608e762acd"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -310,7 +310,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
"-A SnpEff",
1,
Arrays.asList("2a1eced23dd605d1b0a3efde3f04e23f"));
Arrays.asList("81ac0ffd22a0d0907848019944034359"));
executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
}

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
View File

@ -70,7 +70,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("f03e4ef62d6614c9b1b0a600f7e9f16d"));
Arrays.asList("605f447127bf9c92f60bbaa9c6a6732e"));
executeTest("test MultiSample Pilot1", spec);
}
@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("281db46f39e3367f207838c620a82bd2"));
Arrays.asList("e5c34be242c9b6bec687c7384ef83cb2"));
executeTest("test SingleSample Pilot2", spec);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -87,7 +87,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
//TODO this might need to be addressed at some point.
//TODO the following test is commented out for the record
//tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8d30370465d74fd549d76dd31adc4c0c"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "a4286ada7f9efaa83f7a8f0e72c3cb45"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cf5545094ebb264fa8eb879fd848d9ef"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0086cc735cf792a9f236ec057c73b750"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"});

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -107,7 +107,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeBAMOutFlags() throws IOException {
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "a6abb0aa68d3b4d15185a119350e76dc", "d38aab5bf8ef0bc7c18e8c909819da84");
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "700c5d20e9d9d9a431fcda9bff91f72e", "a0daf5a80158d4a462248415c1e17565");
}
@Test
@ -203,7 +203,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3625167f0e788d409c7eab1898d5eafe");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "49b8fb444c6f88def2069b8b0efe47c7");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -361,7 +361,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestAggressivePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("c2dab66ad3740320004874c83051bbfc"));
Arrays.asList("fcc81209c562f3c7f1627b187a4dfab4"));
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
}
@ -369,7 +369,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestConservativePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("a8ea15ac136042891434ccb0b3c3b686"));
Arrays.asList("61aef3fe9d18eec1df526e99a8456115"));
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
}

20
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -108,7 +108,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000", b37KGReference),
1,
Collections.singletonList("b82f29eee8b1369b376ace857bf9b55a"));
Collections.singletonList("7b2a135e694f9d1190e041e6fd420123"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -157,7 +157,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
1,
Collections.singletonList("ea11554de21ef8f25e9983db8b5a8480"));
Collections.singletonList("a9ecd152ec4b5b541887a0aed016f40d"));
spec.disableShadowBCF();
executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
}
@ -171,7 +171,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-20,000,000", b37KGReference),
1,
Collections.singletonList("b304c7e3bb3625a1cdb5531c77b13bcd"));
Collections.singletonList("06e218297fa5399538d13b6a8db4cfe3"));
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
}
@ -183,7 +183,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
1,
Collections.singletonList("08adc638b9539fd275836ed008d900ee"));
Collections.singletonList("181fcb5d240b9bd92e3c793ca5aa7954"));
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
}
@ -251,7 +251,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-allSites"),
1,
Collections.singletonList("764ac46e0b985db187d85655240f7ec0"));
Collections.singletonList("2425f2567bfcf187ebae3fb5fa7558b1"));
spec.disableShadowBCF();
executeTest("testAllSitesNonBiallelic", spec);
}
@ -270,7 +270,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-stand_call_conf 300"),
1,
Collections.singletonList("30903101c5459f602d7004934bc85ca9"));
Collections.singletonList("0ea995f728391647c69f2a3c9a6c1d03"));
executeTest("testStandardConf", spec);
}
@ -310,7 +310,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
" --uniquifySamples", b37KGReference),
1,
Collections.singletonList("1cb3bddf47c620d294b08acd70d35fa3"));
Collections.singletonList("0c99b1b20fb035a5dada036bd4cf39e5"));
executeTest("testUniquifiedSamples", spec);
}
@ -590,7 +590,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" +
" -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" +
" -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames),
Collections.singletonList("e88db6e49c12487c55de42769d2f8c6c"));
Collections.singletonList("903047b6262fcb82070556ff74f26a75"));
spec.disableShadowBCF();
executeTest("testSetZeroRGQsToNoCall", spec);
}
@ -668,7 +668,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testGenotypingSpanningDeletionWithAllSites() {
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "spanningDel.genotyping.g.vcf -allSites", b37KGReference),
Collections.singletonList("d3d862faf954f9bb8b1619c3e889ad8c"));
Collections.singletonList("04cfe93e92444cbde80e13ca8b8c3913"));
spec.disableShadowBCF();
executeTest("testGenotypingSpanningDeletionWithAllSites", spec);
}
@ -686,7 +686,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testNewQualNaNBugFix() {
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -newQual -V " + privateTestDir + "input-newqual-nan-bug-fix.vcf", b37KGReferenceWithDecoy),
Collections.singletonList("503f4193c22fbcc451bd1c425b8b6bf8"));
Collections.singletonList("e1a7801c9bb5e80d204635bac6105abf"));
spec.disableShadowBCF();
executeTest("testNewQualNaNBugFix", spec);
}