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Updating FCPT nCalledLoci due to fixed QD<2.0 filter. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5686 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-04-25 21:37:04 +00:00
parent ed6da6f72d
commit 6ca4e3cebf
1 changed files with 4 additions and 19 deletions
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23
scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
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@ -32,14 +32,14 @@ import org.broadinstitute.sting.utils.yaml.YamlUtils
import org.broadinstitute.sting.queue.pipeline._
class FullCallingPipelineTest {
def datasets = List(k1gChr20Dataset)//, k1gExomeDataset)
def datasets = List(k1gChr20Dataset)
val k1gChr20Dataset = {
val dataset = newK1gDataset("Barcoded_1000G_WEx_chr20", true)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.all", "nCalledLoci", 1398)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.known", "nCalledLoci", 1143)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.novel", "nCalledLoci", 255)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.all", "nCalledLoci", 1391)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.known", "nCalledLoci", 1142)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.novel", "nCalledLoci", 249)
dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.all", "tiTvRatio", 3.6250)
dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.known", "tiTvRatio", 3.7190)
dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.novel", "tiTvRatio", 3.2037)
@ -47,21 +47,6 @@ class FullCallingPipelineTest {
dataset
}
val k1gExomeDataset = {
val dataset = newK1gDataset("Barcoded_1000G_WEx", false)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.all", "nCalledLoci", 52668)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.known", "nCalledLoci", 41248)
dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.novel", "nCalledLoci", 11420)
dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.all", "tiTvRatio", 3.271)
dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.known", "tiTvRatio", 3.3299)
dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.novel", "tiTvRatio", 3.0487)
dataset.jobQueue = "gsa"
dataset
}
def newK1gDataset(projectName: String, chr20: Boolean) = {
val project = PipelineTest.createHg19Project(projectName, chr20)
var samples = List.empty[PipelineSample]