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quick update with the correct CEU trio bam file and it's final location. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5098 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-01-27 19:17:19 +00:00
parent 5ed128f839
commit cae4b9b0de
1 changed files with 1 additions and 1 deletions
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2
scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -112,7 +112,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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),
"WExTrio" -> new Target("NA12878Trio.WEx", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-scr1/carneiro/prj/trio/data/NA12878Trio.WEx.hg19.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"),
"/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)
)