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Added NA12878 Trio dataset to the pipeline. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5037 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-01-20 23:15:33 +00:00
parent 8855f080c2
commit fc73569d62
1 changed files with 2 additions and 42 deletions
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44
scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -55,6 +55,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val goldStandardClusterFile = new File(goldStandardName + ".clusters")
}
val hg19 = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta")
val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
@ -111,52 +112,11 @@ 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/NA12878Trio.WEx.hg19.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/trio/data/NA12878Trio.WEx.hg19.recal.bam"),
new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/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)
)
/*
// OLD TARGET DATABASES -- TO BE REMOVED.
val HiSeq = new Target("NA12878.HiSeq", hg18, "hg18", // BUGBUG: cut down to chr1
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"),
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)
val WEx = new Target("NA12878.WEx", hg18, "hg18",
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, !lowPass)
val LowPassN60 = new Target("lowpass.N60", b36, "b36", // which reference the data is aligned to
new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from
new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), // the gold standard VCF file to run through the VQSR
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, lowPass) // chunked interval list to use with Queue's scatter/gather functionality
val LowPassAugust = new Target("ALL.august.v4", b37, "b37", // BUGBUG: kill this, it is too large
new File("/humgen/1kg/processing/allPopulations_chr20_august_release.cleaned.merged.bams/ALL.cleaned.merged.list"),
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass)
val LowPassEUR363Nov = new Target("EUR.nov2010", b37, "b37",
new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"),
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)
val LowPassFIN79Nov = new Target("FIN.nov2010", b37, "b37",
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
new File("/broad/shptmp/rpoplin/pipeline_newHS7/FIN.nov2010.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass)
val TGPWExGdA = new Target("1000G.WEx.GdA", b37, "b37",
new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), // BUGBUG: reduce from 60 to 20 people
new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/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)
val WExTrio = new Target("NA12878Trio.WEx", b37, "b37",
new File("/humgen/gsa-scr1/carneiro/prj/trio/NA12878Trio.WEx.hg19.bam"),
new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/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)
//val targets = List(HiSeq, WEx, LowPassN60, LowPassAugust, LowPassEUR363Nov, LowPassFIN79Nov, TGPWExGdA)
//val targets = List(HiSeq, WEx, LowPassEUR363Nov, LowPassFIN79Nov)
//val targets = List(LowPassFIN79Nov)
*/
def script = {