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Change default downsampling coverage target for the HaplotypeCaller t…

…o 250

-was previously set to 30, which seems far too aggressive given that with
 ActiveRegionWalkers, as with LocusWalkers, this limits the depth of any
 pileup returned by LIBS

-250 is a more conservative default used by the UG

-can adjust down/up later based on further experiments (GSA-699 will
 remain open)

-verified with Ryan that all integration test differences are either
 innocent or represent an improvement

GSA-699
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commit 8b29030467b0e5e4459d1686a98d17937fc841f1 1 parent 51d618d
@droazen droazen authored
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2  ...ected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -133,7 +133,7 @@
@PartitionBy(PartitionType.LOCUS)
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ActiveRegionTraversalParameters(extension=85, maxRegion=300)
-@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=30)
+@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=250)
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
/**
View
8 ...st/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java
@@ -255,7 +255,7 @@ public void testHCContaminationDownsamplingFlat() {
final String baseCommand = "-T HaplotypeCaller -R " + b36KGReference + " --no_cmdline_in_header --dbsnp " + b36dbSNP129;
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -contamination 0.20", 1,
- Arrays.asList("3a66513cdfef46f315d5ada8a104822f"));
+ Arrays.asList("c3a253467ead7b1cfe9fd9dd310828b1"));
executeTest("HC calling with contamination_percentage_to_filter 0.20", spec);
}
@@ -283,17 +283,17 @@ private void testHCFlatContamination(final String bam1, final String bam2, final
@Test
public void testHCFlatContaminationCase1() {
- testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "9dbd17769e091ce759efda050cd4f8b2");
+ testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "c3e695381d8627e3922d8c642b66c3ce");
}
@Test
public void testHCFlatContaminationCase2() {
- testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "b8cee98c9c693fd336fc5e574dd744ed");
+ testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "002d2b45336d88d7c04e19f9f26e29d9");
}
@Test
public void testHCFlatContaminationCase3() {
- testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "e7309bd594b8e4b54b712f9877518b8e");
+ testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "1809a33ac112d1a3bd7a071c566794dd");
}
}
View
18 ...org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -68,12 +68,12 @@ private void HCTest(String bam, String args, String md5) {
@Test
public void testHaplotypeCallerMultiSample() {
- HCTest(CEUTRIO_BAM, "", "a9748a39604c4ec8bbdb2cb809a971f1");
+ HCTest(CEUTRIO_BAM, "", "aac5517a0a64ad291b6b00825d982f7f");
}
@Test
public void testHaplotypeCallerSingleSample() {
- HCTest(NA12878_BAM, "", "c55ebed976767e1f93d2e8ada9d52bf8");
+ HCTest(NA12878_BAM, "", "3bfab723fb0f3a65998d82152b67ed15");
}
@Test(enabled = false)
@@ -84,7 +84,7 @@ public void testHaplotypeCallerSingleSampleWithDbsnp() {
@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",
- "70a53e566e6a7090e2f29ed608e9d84f");
+ "283524b3e3397634d4cf0dc2b8723002");
}
private void HCTestComplexGGA(String bam, String args, String md5) {
@@ -96,13 +96,13 @@ private void HCTestComplexGGA(String bam, String args, String md5) {
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
- "1d9cd5017e420d5862b7b94e6cb5de3b");
+ "417174e043dbb8b86cc3871da9b50536");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
- "10fdbfeb3b4ea1af7f242a8aca83cb9b");
+ "f2df7a8f53ce449e4a8e8f8496e7c745");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@@ -125,7 +125,7 @@ private void HCTestSymbolicVariants(String bam, String args, String md5) {
// TODO -- need a better symbolic allele test
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
- HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "f893aa7afef71705df7f040b22440a2d");
+ HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "56f2ef9acc6c0d267cf2b7a447d87fb7");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@@ -146,7 +146,7 @@ public void testHaplotypeCallerSingleSampleIndelQualityScores() {
@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("0689d2c202849fd05617648eaf429b9a"));
+ final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ccd30e226f097a40cdeebaa035a290a7"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@@ -175,7 +175,7 @@ public void HCTestDoesNotFailOnBadRefBase() {
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("2ab038f4f6c262b3245b6fa549659c5e"));
+ Arrays.asList("adb08cb25e902cfe0129404a682b2169"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
@@ -183,7 +183,7 @@ public void HCTestReducedBam() {
public void testReducedBamWithReadsNotFullySpanningDeletion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
- Arrays.asList("56fc9110974bfa9c9fe196b0d4af4e64"));
+ Arrays.asList("6debe567cd5ed7eb5756b6605a151f56"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}
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