zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added argument to WGP and HSP to allow more memory. 

Upped the WGP VQSR memory to 32g to power through the filtering whole genome. TODO: Figure out what the right amount is.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5940 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-06-03 20:48:37 +00:00
parent cd293f145b
commit 4c6751ec3c
2 changed files with 16 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
scala/qscript/playground/HybridSelectionPipeline.scala 100755 → 100644
View File

@ -36,21 +36,24 @@ class HybridSelectionPipeline extends QScript {
@Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
var yamlFile: File = _
@Input(doc="level of parallelism for UnifiedGenotyper. By default is set to 20.", shortName="varScatter", required=false)
@Input(doc="level of parallelism for UnifiedGenotyper. By default set to 20.", shortName="varScatter", required=false)
var variantCallerScatterCount = 20
@Argument(doc="memory limit for UnifiedGenotyper. By default is set to 4g.", shortName="varMemory", required=false)
var variantCallerMemory = 4
@Argument(doc="memory limit for UnifiedGenotyper. By default set to 2g.", shortName="varMemory", required=false)
var variantCallerMemory = 2
@Argument(doc="expand each target in input intervals by the specified number of bases (50 bases by default)", shortName="expand", required=false)
@Argument(doc="expand each target in input intervals by the specified number of bases. By default set to 50 bases.", shortName="expand", required=false)
var expandIntervals = 50
@Argument(doc="pipeline memory limit. By default set to 2g.", shortName="pipeMemory", required=false)
var pipelineMemoryLimit = 2
private var pipeline: Pipeline = _
trait CommandLineGATKArgs extends CommandLineGATK {
this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
this.intervals = List(qscript.pipeline.getProject.getIntervalList)
this.memoryLimit = 4
this.memoryLimit = pipelineMemoryLimit
}
def script() {

10
scala/qscript/playground/WholeGenomePipeline.scala
View File

@ -42,6 +42,9 @@ class WholeGenomePipeline extends QScript {
@Argument(doc="Chunk size. Defaults to 3,000,000", shortName="chunk", required=false)
var chunkSize = 3000000
@Argument(doc="Memory limit. Defaults to 4g", shortName="pipeMemory", required=false)
var pipelineMemoryLimit = 4
val resources = "/humgen/gsa-pipeline/resources/5777/b37/"
val reference = resources + "human_g1k_v37.fasta"
val dbsnp = resources + "dbsnp_132.b37.vcf"
@ -52,7 +55,7 @@ class WholeGenomePipeline extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK {
this.reference_sequence = reference
this.intervalsString = runIntervals
this.memoryLimit = 2
this.memoryLimit = pipelineMemoryLimit
}
case class Interval(chr: String, start: Long, stop: Long) {
@ -214,6 +217,7 @@ class WholeGenomePipeline extends QScript {
vr.tranches_file = projectBase + ".tranches"
vr.recal_file = projectBase + ".recal"
vr.jobOutputFile = vr.recal_file + ".out"
vr.memoryLimit = 32
add(vr)
for (tranche <- vr.TStranche) {
@ -224,6 +228,7 @@ class WholeGenomePipeline extends QScript {
ar.ts_filter_level = tranche.toDouble
ar.out = projectBase + ".recalibrated." + tranche + ".vcf"
ar.jobOutputFile = ar.out + ".out"
ar.memoryLimit = 32
add(ar)
val eval = new VariantEval with CommandLineGATKArgs
@ -233,9 +238,10 @@ class WholeGenomePipeline extends QScript {
eval.doNotUseAllStandardStratifications = true
eval.doNotUseAllStandardModules = true
eval.evalModule = List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants")
eval.stratificationModule = List("EvalRod", "CompRod", "Novelty", "Filter", "FunctionalClass", "Sample")
eval.stratificationModule = List("EvalRod", "CompRod", "Novelty")
eval.out = swapExt(ar.out, ".vcf", ".eval")
eval.jobOutputFile = eval.out + ".out"
eval.memoryLimit = 32
add(eval)
}
}