From ed402588cc37c0bc1b979916f4e623a7671065f4 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 20 Oct 2011 16:19:13 -0400 Subject: [PATCH] Adding the "gold standard NA12878" target --- .../qscripts/MethodsDevelopmentCallingPipeline.scala | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala index cc4790f05..88c1bd2c8 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -98,13 +98,17 @@ class MethodsDevelopmentCallingPipeline extends QScript { // BUGBUG: We no longer support b36/hg18 because several of the necessary files aren't available aligned to those references val targetDataSets: Map[String, Target] = Map( + "NA12878_gold" -> new Target("NA12878.goldStandard", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, + new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/data/goldStandard.list"), + new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** There is no gold standard for the gold standard ** + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, lowPass, !exome, 391), "NA12878_wgs_b37" -> new Target("NA12878.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"), + new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1), "NA12878_wgs_decoy" -> new Target("NA12878.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** + new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1), "NA12878_wgs_hg18" -> new Target("NA12878.HiSeq.WGS.hg18", hg18, dbSNP_hg18_129, hapmap_hg18, "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask", @@ -142,7 +146,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3), "GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"), + new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.GA2.hg19.filtered.vcf"), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1), "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37, new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),