From 6308b0f0365144dbb0e207211fef1fbe32cc405b Mon Sep 17 00:00:00 2001 From: Takuto Sato Date: Wed, 24 Feb 2016 15:06:57 -0500 Subject: [PATCH] Add MuTect2 Tumor-only test. --- .../cancer/m2/MuTect2IntegrationTest.java | 22 ++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java index f9b18d4b9..1d324ed71 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java @@ -89,6 +89,18 @@ public class MuTect2IntegrationTest extends WalkerTest { executeTest("testM2: args=" + args, spec); } + private void m2TumorOnlyTest(String tumorBam, String intervals, String args, String md5) { + final String base = String.format( + "-T MuTect2 --no_cmdline_in_header -dt NONE --disableDithering -alwaysloadVectorHMM -pairHMM LOGLESS_CACHING -ip 50 -R %s --dbsnp %s --cosmic %s --normal_panel %s -I:tumor %s -L %s", + REF, DBSNP, COSMIC, PON, tumorBam, intervals) + + " -o %s "; + + final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5)); + + spec.disableShadowBCF(); + executeTest("testM2TumorOnly: args=" + args, spec); + } + @Test public void testMicroRegression() { M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "617054c6d056cad7448a463cb8d04a55"); @@ -113,7 +125,7 @@ public class MuTect2IntegrationTest extends WalkerTest { M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "11357aa543e7c6b2725cd330adba23a0"); } - /* + /** * Test that contamination downsampling reduces tumor LOD, rejects more variants */ @Test @@ -121,4 +133,12 @@ public class MuTect2IntegrationTest extends WalkerTest { M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "d7947ddf0240fe06a44621312831f44c"); } + /** + * Test that tumor-only mode does not create an empty vcf + */ + @Test + public void testTumorOnly(){ + m2TumorOnlyTest(CCLE_MICRO_TUMOR_BAM, "2:166000000-167000000", "", "8439d9a673b3a57aa5893af600125d3b"); + } + }