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Add MuTect2 Tumor-only test.

This commit is contained in:
Takuto Sato 2016-02-24 15:06:57 -05:00
parent d0432713e0
commit 6308b0f036
1 changed files with 21 additions and 1 deletions
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22
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java
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@ -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");
}
}