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Added a ten sample 1000G whole exome test along with SimpleMetricsBySample to the pipeline validation. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4737 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-11-26 23:17:23 +00:00
parent e3e6d176df
commit 6f8cd97673
1 changed files with 28 additions and 10 deletions
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38
scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
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@ -11,16 +11,40 @@ import java.text.SimpleDateFormat
import java.util.Date import java.util.Date
class FullCallingPipelineTest extends BaseTest { class FullCallingPipelineTest extends BaseTest {
def datasets = List(k1gChr20Dataset) def datasets = List(k1gChr20Dataset, k1gExomeDataset)
private final val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/" private final val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/"
val k1gChr20Dataset = { val k1gChr20Dataset = {
val dataset = newK1gDataset
dataset.pipeline.getProject.setName("Barcoded_1000G_WEx_chr20")
dataset.pipeline.getProject.setIntervalList(new File(BaseTest.GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list"))
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.counter.nCalledLoci", "1390", "1420")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.titv.tiTvRatio", "3.52", "3.60")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.known.titv.tiTvRatio", "3.71", "3.80")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.novel.titv.tiTvRatio", "2.79", "2.86")
dataset
}
val k1gExomeDataset = {
val dataset = newK1gDataset
dataset.pipeline.getProject.setName("Barcoded_1000G_WEx")
dataset.pipeline.getProject.setIntervalList(new File(BaseTest.GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list"))
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.counter.nCalledLoci", "51969", "53019")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.titv.tiTvRatio", "3.18", "3.25")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.known.titv.tiTvRatio", "3.29", "3.36")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.novel.titv.tiTvRatio", "2.80", "2.87")
dataset
}
def newK1gDataset = {
val project = new PipelineProject val project = new PipelineProject
project.setName("Barcoded_1000G_WEx_chr20")
project.setReferenceFile(new File(BaseTest.hg19Reference)) project.setReferenceFile(new File(BaseTest.hg19Reference))
project.setDbsnpFile(new File(BaseTest.b37dbSNP129)) project.setDbsnpFile(new File(BaseTest.b37dbSNP129))
project.setIntervalList(new File(BaseTest.GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list"))
val squid = "C426" val squid = "C426"
val ids = List( val ids = List(
@ -43,12 +67,6 @@ class FullCallingPipelineTest extends BaseTest {
dataset.pipeline = pipeline dataset.pipeline = pipeline
dataset.refseq = BaseTest.hg19Refseq dataset.refseq = BaseTest.hg19Refseq
dataset.targetTiTv = "3.0" dataset.targetTiTv = "3.0"
dataset.jobQueue = "hour"
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.counter.nCalledLoci", "1390", "1420")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.titv.tiTvRatio", "3.52", "3.60")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.known.titv.tiTvRatio", "3.71", "3.80")
dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.novel.titv.tiTvRatio", "2.79", "2.86")
dataset dataset
} }
@ -84,7 +102,7 @@ class FullCallingPipelineTest extends BaseTest {
val optimizedVcf = PipelineTest.runDir(testName) + "SnpCalls/%s.uncleaned.annotated.indel.masked.recalibrated.tranched.vcf".format(projectName) val optimizedVcf = PipelineTest.runDir(testName) + "SnpCalls/%s.uncleaned.annotated.indel.masked.recalibrated.tranched.vcf".format(projectName)
// eval modules to record in the validation directory // eval modules to record in the validation directory
val evalModules = List("CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator") val evalModules = List("CompOverlap", "CountFunctionalClasses", "CountVariants", "SimpleMetricsBySample", "TiTvVariantEvaluator")
// write the report to the shared validation data location // write the report to the shared validation data location
val formatter = new SimpleDateFormat("yyyy.MM.dd.HH.mm.ss") val formatter = new SimpleDateFormat("yyyy.MM.dd.HH.mm.ss")