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wex is wex, wgs is wgs.... i think i got it right this time. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5828 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-05-20 16:44:25 +00:00
parent e16bc2cbd9
commit 3a2e32eef3
1 changed files with 2 additions and 2 deletions
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4
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -125,11 +125,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"),
new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"),
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, 97.0, !lowPass),
"WExTrio" -> new Target("CEUTrio.WGS", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
"WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/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, 97.0, !lowPass),
"WGSTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
"WGSTrio" -> new Target("CEUTrio.WGS", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass),