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Committing my notes about the methods development pipeline so we stay synced up while I'm on vacation. Cheers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4891 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-12-21 21:14:20 +00:00
parent cc909602c7
commit 7185fcb47b
1 changed files with 17 additions and 7 deletions
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24
scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -31,9 +31,19 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta")
val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
// ToDos:
// reduce the scope of the datasets so the script is more nimble
// figure out how to give names to all the Queue-LSF logs (other than Q-1931@node1434-24.out) so that it is easier to find logs for certain steps
// create gold standard BAQ'd bam files, no reason to always do it on the fly
// Analysis to add at the end of the script:
// auto generation of the cluster plots
// spike in NA12878 to the exomes and to the lowpass, analysis of how much of her variants are being recovered compared to single sample exome or HiSeq calls
// produce Kiran's Venn plots based on comparison between new VCF and gold standard produced VCF
// Define the target datasets here
def lowPass = true
val HiSeq = new Target("NA12878.HiSeq", hg18, "hg18",
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)
@ -41,11 +51,11 @@ 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, !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 compare against
"/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",
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)
@ -58,7 +68,7 @@ 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)
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"),
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)