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updated to work with the new VariantEval. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5176 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-02 17:46:07 +00:00
parent 47357b726e
commit cf15819db5
1 changed files with 7 additions and 9 deletions
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16
scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -111,9 +111,9 @@ class MethodsDevelopmentCallingPipeline extends QScript {
new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"), new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"),
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
"WExTrio" -> new Target("NA12878Trio.WEx", b37, dbSNP_b37, hapmap_b37, indelMask_b37, "WExTrio" -> new Target("CEUTrio.WEx", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/trio/snps/NA12878Trio.WEx.filtered.vcf"), new File("/humgen/gsa-scr1/carneiro/prj/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass) "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass)
) )
@ -247,20 +247,18 @@ class MethodsDevelopmentCallingPipeline extends QScript {
} }
// 5.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf // 5.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf
class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS { class VariantEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
val name: String = t.name val name: String = t.name
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile) this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
this.rodBind :+= RodBind("eval", "VCF", t.tsRecalibratedVCF) this.rodBind :+= RodBind("eval", "VCF", t.tsRecalibratedVCF)
this.analysisName = name + "_VR" this.analysisName = name + "_VR"
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R) this.EV ++= List("GenotypeConcordance", "PrintMissingComp")
this.reportLocation = new File(t.name + ".eval") this.out = new File(this.name + ".eval")
this.noStandard = true
this.evalModule ++= List("TiTvVariantEvaluator", "CountVariants", "GenotypeConcordance")
if (t.dbsnpFile.endsWith(".rod")) if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile) this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf")) else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
} }
} }