The QD normalization for indels was busted and is now fixed.
It is true that indels of length > 1 have higher QUALS than those of length = 1. But for the HC those QUALS are not that much higher, and it doesn't continue scaling up as the indels get larger. So we no longer normalize by indel length (which massively over-penalizes larger events and effectively drops their QD to 0). For the UG the previous normalization also wasn't perfect. Now we divide the indel length by a factor of 3 to make sure that QD is consistent over the range of indel lengths. Integration tests change because QD is different for indels. Also, got permission from Valentin to archive a failing test that no longer applies. Thanks to Kurt on the GATK forum for pointing this all out.
This commit is contained in:
Eric Banks
parent
c86e36c909
commit
c7e08965d0
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@ -108,7 +108,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
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continue;
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depth += perReadAlleleLikelihoods.getNumberOfStoredElements();
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} else if (genotype.hasDP() && vc.isBiallelic()) { // TODO -- this currently only works with biallelic variants for now because multiallelics have had their PLs stripped out and therefore their qual score can't be recomputed
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} else if ( genotype.hasDP() ) {
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depth += genotype.getDP();
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}
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}
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@ -117,13 +117,29 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
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return null;
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final double altAlleleLength = GATKVariantContextUtils.getMeanAltAlleleLength(vc);
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double QD = -10.0 * vc.getLog10PError() / ((double)depth * altAlleleLength);
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// Hack: when refContext == null then we know we are coming from the HaplotypeCaller and do not want to do a
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// full length-based normalization (because the indel length problem is present only in the UnifiedGenotyper)
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double QD = -10.0 * vc.getLog10PError() / ((double)depth * indelNormalizationFactor(altAlleleLength, ref != null));
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// Hack: see note in the fixTooHighQD method below
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QD = fixTooHighQD(QD);
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Map<String, Object> map = new HashMap<>();
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final Map<String, Object> map = new HashMap<>();
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map.put(getKeyNames().get(0), String.format("%.2f", QD));
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return map;
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}
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/**
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* Generate the indel normalization factor.
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*
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* @param altAlleleLength the average alternate allele length for the call
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* @param increaseNormalizationAsLengthIncreases should we apply a normalization factor based on the allele length?
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* @return a possitive double
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*/
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private double indelNormalizationFactor(final double altAlleleLength, final boolean increaseNormalizationAsLengthIncreases) {
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return ( increaseNormalizationAsLengthIncreases ? Math.max(altAlleleLength / 3.0, 1.0) : 1.0);
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}
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/**
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* The haplotype caller generates very high quality scores when multiple events are on the
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* same haplotype. This causes some very good variants to have unusually high QD values,
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@ -358,7 +358,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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final File outputVCFNoQD = executeTest("testQualByDepth calling without QD", specNoQD).getFirst().get(0);
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final String baseAnn = String.format("-T VariantAnnotator -R %s -V %s", REF, outputVCFNoQD.getAbsolutePath()) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -A QualByDepth";
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final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("139a4384f5a7c1f49ada67f416642249"));
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final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("0c331915b07b42d726bc3d623aa9997b"));
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specAnn.disableShadowBCF();
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final File outputVCFAnn = executeTest("testQualByDepth re-annotation of QD", specAnn).getFirst().get(0);
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@ -384,10 +384,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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Assert.assertFalse(lineAnn == null);
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final VariantContext vcAnn = codecAnn.decode(lineAnn);
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if( vc.isBiallelic() ) {
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Assert.assertTrue(vc.hasAttribute("QD"));
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Assert.assertTrue(vcAnn.hasAttribute("QD"));
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}
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Assert.assertTrue(vc.hasAttribute("QD"));
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Assert.assertTrue(vcAnn.hasAttribute("QD"));
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}
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Assert.assertFalse(lineIterator.hasNext());
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@ -69,16 +69,16 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
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@Test(enabled = true)
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public void testBOTH_GGA_Pools() {
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "dac2d7969e109aee9ad2dad573759f58");
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "0eec36459cf1f1e3e8739ab5b1cedb39");
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}
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@Test(enabled = true)
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public void testINDEL_GGA_Pools() {
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "ceb105e3db0f2b993e3d725b0d60b6a3");
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "73229442a8fe558e58dd5dd305eb2315");
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}
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "4dd1b38f0389e339ce8a05956956aa8a");
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "2787064918c7b391071a6ad4e5b0aba8");
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}
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}
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@ -58,7 +58,7 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","39f559996f8d429839c585bbab68dbde");
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","50ebb7f74e5618acdd014dd87f2363fc");
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}
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@Test(enabled = true)
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@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("3c8727ee6e2a6f10ab728c4869dd5b92"));
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Arrays.asList("1ad3943ae27a0062c52a19abe1c0d32c"));
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executeTest(String.format("test indel caller in SLX"), spec);
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}
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@ -88,7 +88,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -minIndelCnt 1" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("0cbe889e03bab6512680ecaebd52c536"));
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Arrays.asList("9b4ead3da021763704fcb9d80a5ee6ff"));
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executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
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}
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@ -101,7 +101,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("e10c49fcf9a128745c2b050a52798e58"));
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Arrays.asList("8a0a751afdb2a8166432d9822e4d814c"));
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executeTest(String.format("test indel calling, multiple technologies"), spec);
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}
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@ -111,7 +111,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("475f8148123792064130faf9f9030fec"));
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Arrays.asList("422a114943a9e3e9bf5872b82cbc6340"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
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}
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@ -121,7 +121,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
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+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("a7e4e1bd128424d46cffdd538b220074"));
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Arrays.asList("01fec03933816e8d82aabe6e5b276dd5"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
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}
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@ -136,7 +136,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
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"low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
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Arrays.asList("903af514f70db9238064da311c4ea0de"));
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Arrays.asList("e3c95f745ebf2d4f26759878966c5280"));
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executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
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}
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@ -176,7 +176,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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public void testMinIndelFraction0() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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assessMinIndelFraction + " -minIndelFrac 0.0", 1,
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Arrays.asList("d3721bee5edaa31fdd35edd7aa75feb3"));
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Arrays.asList("4a45d5bd459565ec35c726894430e8df"));
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executeTest("test minIndelFraction 0.0", spec);
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}
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@ -184,7 +184,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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public void testMinIndelFraction25() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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assessMinIndelFraction + " -minIndelFrac 0.25", 1,
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Arrays.asList("a5b6d7b32953500d936d3dff512a6254"));
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Arrays.asList("a78c663eff00b28b44f368f03b2acf1b"));
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executeTest("test minIndelFraction 0.25", spec);
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}
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@ -182,12 +182,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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// --------------------------------------------------------------------------------------------------------------
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@Test
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public void testHeterozyosity1() {
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testHeterozosity( 0.01, "2f3051caa785c7c1e2a8b23fa4da90b1" );
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testHeterozosity( 0.01, "6053106407e09a6aefb78395a0e22ec4" );
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}
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@Test
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public void testHeterozyosity2() {
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testHeterozosity( 1.0 / 1850, "228df9e38580d8ffe1134da7449fa35e" );
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testHeterozosity( 1.0 / 1850, "37666375278259c4d7dc800a0f73c1ca" );
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}
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private void testHeterozosity(final double arg, final String md5) {
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@ -203,7 +203,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "eebec02fdde9937bffaf44902ace6207";
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private final static String COMPRESSED_OUTPUT_MD5 = "c5c6af421cffa12fe6bdaced6cd41dd2";
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@Test
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public void testCompressedOutput() {
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@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("c4248f02103e37e89b0f22c0d9c98492"));
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Arrays.asList("630d1dcfb7650a9287d6723c38b0746a"));
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executeTest(String.format("test multiple technologies"), spec);
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}
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@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -L 1:10,000,000-10,100,000" +
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" -baq CALCULATE_AS_NECESSARY",
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1,
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Arrays.asList("96c7862d55e933b274cabe45c9c443d9"));
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Arrays.asList("976e88e4accb4436ad9ac97df9477648"));
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executeTest(String.format("test calling with BAQ"), spec);
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}
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@ -88,7 +88,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testSingleSamplePilot2() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
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Arrays.asList("02b521fe88a6606a29c12c0885c3debd"));
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Arrays.asList("75503fce7521378f8c2170094aff29df"));
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executeTest("test SingleSample Pilot2", spec);
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}
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@ -112,7 +112,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testReverseTrim() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
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Arrays.asList("a973298b2801b80057bea88507e2858d"));
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Arrays.asList("02c7804c8013ba1ead8e02b956b5e454"));
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executeTest("test reverse trim", spec);
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}
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@ -74,7 +74,7 @@ public class UnifiedGenotyperReducedReadsIntegrationTest extends WalkerTest {
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@Test
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public void testReducedBamINDELs() {
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testReducedCalling("INDEL", "942930038cf7fc9a80b969461aaa9aa6");
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testReducedCalling("INDEL", "d593628b2bc144e987a9e75e5eee0001");
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}
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@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleComplex1() {
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "88c10027c21712b1fe475c06cadd503c");
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "ff19ae39b0695680ea670d53f6f9ce47");
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}
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private void HCTestSymbolicVariants(String bam, String args, String md5) {
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@ -65,9 +65,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
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final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
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// this functionality can be adapted to provide input data for whatever you might want in your data
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ce9c42e7e97a45a82315523dbd77fcf"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "c5a55196e10680a02c833a8a44733306"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "9b9923ef41bfc7346c905fdecf918f92"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.NONE, PCRFreeIntervals, "96328c91cf9b06de231b37a22a7a7639"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ac25e9a78b89655197513bb0eb7a6845"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "dc0dde72131d562587acae967cf2031f"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.NONE, WExIntervals, "7cb1e431119df00ec243a6a115fa74b8"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "90e22230149e6c32d1115d0e2f03cab1"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.GVCF, WExIntervals, "b39a4bc19a0acfbade22a011cd229262"});
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@ -84,22 +84,22 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerMultiSample() {
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HCTest(CEUTRIO_BAM, "", "c0b1b64c6005cd3640ffde5dbc10174b");
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HCTest(CEUTRIO_BAM, "", "f2ad35b5e0d181fb18da86a8971ce4f4");
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}
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@Test
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public void testHaplotypeCallerSingleSample() {
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HCTest(NA12878_BAM, "", "439ce9024f04aad08eab1526d887e295");
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HCTest(NA12878_BAM, "", "06abde3268336a7cdb21970f12e819ba");
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}
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@Test
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public void testHaplotypeCallerGraphBasedSingleSample() {
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HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "213df0bdaa78a695e9336128333e4407");
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HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "3d1cb9acdf66547f88ad1742e8178044");
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}
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@Test
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public void testHaplotypeCallerGraphBasedMultiSample() {
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HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ceee711cac50b4bb66a084acb9264941");
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HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "af6f1f504ad771201aedc0157de8830a");
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}
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@Test(enabled = false) // can't annotate the rsID's yet
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@ -110,7 +110,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGA() {
|
||||
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
|
||||
"b09437f11db40abd49195110e50692c2");
|
||||
"fd43de437bbaf960499f67daedc6ef63");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -126,7 +126,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "c57c463542304fb7b2576e531faca89e");
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3a3bb5f0bcec603287520841c559638f");
|
||||
}
|
||||
|
||||
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
|
||||
|
|
@ -173,7 +173,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestProblematicReadsModifiedInActiveRegions() {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -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("976463812534ac164a64c5d0c3ec988a"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("170896ddcfe06ec47e08aefefd99cf78"));
|
||||
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
|
||||
}
|
||||
|
||||
|
|
@ -244,7 +244,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestDBSNPAnnotationWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
Arrays.asList("a43d6226a51eb525f0774f88e3778189"));
|
||||
Arrays.asList("6ab05a77d2e79d21ba85fadf844a13ba"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -261,7 +261,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestDBSNPAnnotationWGSGraphBased() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
Arrays.asList("a6c4d5d2eece2bd2c51a81e34e80040f"));
|
||||
Arrays.asList("903af86b396ce88a6c8e4f4016fbe769"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -293,7 +293,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestAggressivePcrIndelModelWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
|
||||
Arrays.asList("19c2992541ede7407192660fdc1fadbf"));
|
||||
Arrays.asList("824188743703bc09225c5b9c6b404ac1"));
|
||||
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -301,7 +301,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestConservativePcrIndelModelWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
|
||||
Arrays.asList("f4ab037915db3a40ba26e9ee30d40e16"));
|
||||
Arrays.asList("14de866430f49c0026aafc1e34ed8250"));
|
||||
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue