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Adding the "gold standard NA12878" target

This commit is contained in:
Mauricio Carneiro 2011-10-20 16:19:13 -04:00
parent c27e2fb676
commit ed402588cc
1 changed files with 7 additions and 3 deletions
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10
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -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"),