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Put a band-aid on the FCP by switching use of DINDEL to INDEL and explicitly running UG the old way with just indels and just snps. 

Switched YAML parser to new Broad parser which will additionally update picard cleaned bams to the latest version if the project and sample are specified.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5634 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-04-14 02:22:31 +00:00
parent 2089c3bdef
commit 475ad1259d
2 changed files with 6 additions and 5 deletions
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9
scala/qscript/playground/FullCallingPipeline.q
View File

@ -8,7 +8,7 @@ import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, Cl
import org.broadinstitute.sting.queue.library.ipf.intervals.ExpandIntervals
import org.broadinstitute.sting.queue.QScript
import collection.JavaConversions._
import org.broadinstitute.sting.utils.yaml.YamlUtils
import org.broadinstitute.sting.utils.broad.PicardPipeline
class FullCallingPipeline extends QScript {
qscript =>
@ -49,8 +49,8 @@ class FullCallingPipeline extends QScript {
// ------------ SETUP THE PIPELINE ----------- //
def script = {
pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile)
def script() {
pipeline = PicardPipeline.parse(qscript.yamlFile)
val projectBase: String = qscript.pipeline.getProject.getName
@ -175,7 +175,7 @@ class FullCallingPipeline extends QScript {
indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.indels.out")
indels.memoryLimit = 6
indels.downsample_to_coverage = 600
indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL
indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
indels.input_file = bamFiles
indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
indels.out = new File("IndelCalls", base+".indels.vcf")
@ -213,6 +213,7 @@ class FullCallingPipeline extends QScript {
snps.memoryLimit = 6
snps.downsample_to_coverage = 600
snps.input_file = bamFiles
snps.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
snps.out = new File("SnpCalls", base+".snps.vcf")

2
scala/test/org/broadinstitute/sting/queue/pipeline/playground/MultiFullCallingPipelineTest.scala
View File

@ -54,7 +54,7 @@ class MultiFullCallingPipelineTest {
final def convertDatasets: Array[Array[AnyRef]] =
datasets.map(dataset => Array(dataset.asInstanceOf[AnyRef])).toArray
@Test(dataProvider="datasets", enabled=false)
@Test(dataProvider="datasets")
def testMultiFullCallingPipeline(dataset: MultiPipelineDataset) {
val projectName = dataset.name
val testName = "MultiFullCallingPipeline-" + projectName