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Turning on BAQ in Methods Development pipeline. A new dataset is added: 363 EUR samples from the November 1000G release. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4877 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-12-19 21:13:25 +00:00
parent 8118a439c0
commit 34ab5b4889
1 changed files with 20 additions and 10 deletions
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30
scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -18,7 +18,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(4); }
class Target(val baseName: String, val reference: File, val rodName: String, val bamList: File, val goldStandard_VCF: File, val intervals: String, val titvTarget: Double) {
class Target(val baseName: String, val reference: File, val rodName: String, val bamList: File, val goldStandard_VCF: File, val intervals: String, val titvTarget: Double, val isLowpass: Boolean) {
def name = qscript.outputDir + baseName
def clusterFile = new File(name + ".clusters")
def rawVCF = new File(name + ".raw.vcf")
@ -32,32 +32,37 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
// Define the target datasets here
def lowPass = true
val HiSeq = new Target("NA12878.HiSeq", hg18, "hg18",
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.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)
"/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)
"/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) // chunked interval list to use with Queue's scatter/gather functionality
"/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",
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)
"/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("/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)
"/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/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)
"/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, LowPassFIN79Nov, TGPWExGdA)
val targets = List(HiSeq, WEx, LowPassN60, LowPassAugust, LowPassEUR363Nov, LowPassFIN79Nov, TGPWExGdA)
def script = {
def goldStandard = true
@ -85,10 +90,15 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.reference_sequence = t.reference
this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
this.intervalsString ++= List(t.intervals)
this.scatterCount = 50
this.dcov = Some(250)
this.scatterCount = 64
if( t.isLowpass ) {
this.dcov = Some(50)
} else {
this.dcov = Some(250)
}
this.input_file :+= t.bamList
this.out = t.rawVCF
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE)
this.analysisName = t.name + "_UG"
}