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Enabled a whole other bunch of integration tests for BQSRv2. While I was there I also changed the default context size for indels to 3 (from 8) since that's what works best in the current implementation (as suggested by Ryan). At this point, all of the new core tools (ReduceReads, BQSRv2, HaplotypeCaller, UG extensions) have been moved over to protected and should be stable. Looks like we are pretty much ready for GATK 2.0!

This commit is contained in:
Eric Banks 2012-07-17 23:36:43 -04:00
parent a8d08ea18d
commit e4db8dde91
2 changed files with 14 additions and 15 deletions
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27
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -39,21 +39,20 @@ public class BQSRIntegrationTest extends WalkerTest {
String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
String HiSeqInterval = "chr1:10,000,000-10,100,000";
return new Object[][]{
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "93c63489bf274f68e0378a6c296b2948")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "3bb9f93dc5a2eb879099402faf352a01")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "c1321f6548bd240b174a8afe62bb07b9")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "087dbc3e3f0cee6b891aecad2d0faf25")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "8a69591f728b3a2cdd79ff26bbebcc26")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "73d649bce0b69f56452de8c7e0a8686d")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "d9512cebf54ea120539059976b33d1ca")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "b29f83d42fc796b60ebe14a768e4f3af")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "afa916b4d3a57d62b9b3e4f64b97f428")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "5e305384496fb5ff64f7494092c939cf")},
//{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "1:10,000,000-10,200,000", "", "")},
//{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "")},
//{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "1:10,000,000-10,200,000", "", "")},
//{new BQSRTest(b36KGReference, validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "1:10,800,000-10,810,000", "", "")},
//{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "1:1-1,000", " -OQ", "")},
//{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "")},
//{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "")},
//{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "recalibrationTest.bed", "")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "f61a8df03aae8c4273acf2b72497f154")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "7c2ce84e521d8f19fe5061b4e40317f7")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "66a0caad65ab41d9013e812617e67370")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "6f5e9836147b488a7a204cffa5ecd21e")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "444fdfca7835e6a3714445f7e60abcaf")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "e0bfaf38f45142d45c8fe0ae05d0d4e0")},
{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "5b30760bab51b4d1fc02097d4eacefa4")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "742fd8edfa36ab9023ceeaac40c4e215")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "6f5e9836147b488a7a204cffa5ecd21e")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "22dd42897cf20852712c6e8f63195443")},
};
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
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@ -120,7 +120,7 @@ public class RecalibrationArgumentCollection {
* The context covariate will use a context of this size to calculate it's covariate value for base insertions and deletions
*/
@Argument(fullName = "indels_context_size", shortName = "ics", doc = "size of the k-mer context to be used for base insertions and deletions", required = false)
public int INDELS_CONTEXT_SIZE = 8;
public int INDELS_CONTEXT_SIZE = 3;
/**
* A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off (default is off)