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Updating the HC integration test md5s. According to the NA12878 knowledge base this commit cuts down the FP rate by more than 50 percent with no loss in sensitivity.

This commit is contained in:
Ryan Poplin 2012-12-03 15:38:59 -05:00
parent a47da9bb2f
commit d5ed184691
1 changed files with 9 additions and 9 deletions
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18
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -21,19 +21,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "2b39732ff8e0de5bc2ae949aaf7a6f21");
HCTest(CEUTRIO_BAM, "", "d602d40852ad6d2d094be07e60cf95bd");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "8b217638ff585effb9cc70e9a9aa544f");
HCTest(NA12878_BAM, "", "70ad9d53dda4d302b879ca2b7dd5b368");
}
// TODO -- add more tests for GGA mode, especially with input alleles that are complex variants and/or not trimmed
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"541aa8291f03ba33bd1ad3d731fd5657");
"e2b3bf420c45c677956a2e4a56d75ea2");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -44,7 +44,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "fd7170cbde7df04d4fbe1da7903c31c6");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "883871f8bb4099f69fd804f8a6181954");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -55,7 +55,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "99456fc7207c1fe9f367a0d0afae87cd");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "338ab3b7dc3d54df8af94c0811028a75");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -66,20 +66,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "6c1631785b3f832aecab1a99f0454762");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "aff11b014ca42bfa301bcced5f5e54dd");
}
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -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("ec437d2d9f3ae07d155983be0155c8ed"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("2f4ed6dc969bee041215944a9b24328f"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("237601bbc39694c7413a332cbb656c8e"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("d8d6f2ebe79bca81c8a0911daa153b89"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -93,7 +93,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("40bf739fb2b1743642498efe79ea6342"));
Arrays.asList("d01cb5f77ed5aca1d228cfbce9364c21"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
}