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Following Ryan's suggestion, I am moving the Methods Development Calling pipeline to the Core. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5226 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-10 17:36:05 +00:00
parent 9c2c5efe35
commit c630701a76
1 changed files with 4 additions and 3 deletions
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7
scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala → scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -1,3 +1,4 @@
import org.broadinstitute.sting.gatk.CommandLineGATK
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
@ -100,8 +101,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass),
"HiSeq19" -> new Target("NA12878.hg19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, "HiSeq19" -> new Target("NA12878.hg19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/seq/picard_aggregation/G2946/NA12878/v8/NA12878.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.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-scr1/carneiro/prj/hiseq19/analysis/snps/NA12878.hg19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass), // ** we need a chunked hg19 whole genome intervals file ** "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass), // ** we need a chunked hg19 whole genome intervals file **
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37, "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"), new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
@ -281,7 +282,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
} }
// 6.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf // 6.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf
class VariantEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS { class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.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("comphapmap", "VCF", t.hapmapFile) this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)