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small updates to the variant eval part of the pipeline, some updates to the pacbio specific pipeline. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5244 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-15 16:19:07 +00:00
parent 356eb264ab
commit 87e19a17ae
2 changed files with 41 additions and 31 deletions
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7
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
View File

@ -1,4 +1,4 @@
import org.broadinstitute.sting.gatk.CommandLineGATK
import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
@ -285,7 +285,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS {
val name: String = t.name
this.reference_sequence = t.reference
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
this.knownName ++= List("hapmap")
this.rodBind :+= RodBind("eval", "VCF", if (!noCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
this.analysisName = name + "_VE"
this.intervalsString ++= List(t.intervals)
@ -293,7 +294,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.out = t.evalFile
if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))
else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
}
}

65
scala/qscript/oneoffs/carneiro/pbCalling.scala
View File

@ -20,9 +20,6 @@ class pbCalling extends QScript {
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); }
class Target(
val baseName: String,
val reference: File,
@ -33,7 +30,8 @@ class pbCalling extends QScript {
val goldStandard_VCF: File,
val intervals: String,
val titvTarget: Double,
val isLowpass: Boolean) {
val isLowpass: Boolean,
val isCCS: Boolean) {
val name = qscript.outputDir + baseName
val clusterFile = new File(name + ".clusters")
val rawVCF = new File(name + ".raw.vcf")
@ -73,62 +71,63 @@ class pbCalling extends QScript {
// produce Kiran's Venn plots based on comparison between new VCF and gold standard produced VCF
val lowPass: Boolean = true
val ccs: Boolean = true
val targetDataSets: Map[String, Target] = Map(
"HiSeq" -> new Target("NA12878.HiSeq", hg18, dbSNP_hg18, hapmap_hg18,
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
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),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass, !ccs),
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_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, lowPass),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass, !ccs),
"WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18, hapmap_hg18,
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask",
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),
"/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, !ccs),
"TGPWExGdA" -> new Target("1000G.WEx.GdA", b37, dbSNP_b37, hapmap_b37, indelMask_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),
"/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, !ccs),
"LowPassN60" -> new Target("lowpass.N60", b36, dbSNP_b36, hapmap_b36, indelMask_b36,
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
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, lowPass, !ccs), // chunked interval list to use with Queue's scatter/gather functionality
"LowPassAugust" -> new Target("ALL.august.v4", b37, dbSNP_b37, hapmap_b37, indelMask_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),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass, !ccs),
"LowPassEUR363Nov" -> new Target("EUR.nov2010", b37, dbSNP_b37, hapmap_b37, indelMask_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),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass, !ccs),
"WExTrio" -> new Target("NA12878Trio.WEx", b37, 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-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),
"/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, !ccs),
"pacbio" -> new Target("pacbio", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pacbio.filtered.vcf"),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.hg19.intervals", 1.8, !lowPass),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.hg19.intervals", 1.8, !lowPass, !ccs),
"pb200" -> new Target("pb200", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pb200.filtered.vcf"),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.hg19.intervals", 1.8, !lowPass),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.hg19.intervals", 1.8, !lowPass, !ccs),
"pb2k" -> new Target("pb2k", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pb2k.filtered.vcf"),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.hg19.intervals", 1.8, !lowPass),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.hg19.intervals", 1.8, !lowPass, !ccs),
"cc200" -> new Target("cc200", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/cc200.filtered.vcf"),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.hg19.intervals", 1.8, !lowPass),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.hg19.intervals", 1.8, !lowPass, ccs),
"cc2k" -> new Target("cc2k", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.recal.bam"),
new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/cc2k.filtered.vcf"),
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.hg19.intervals", 1.8, !lowPass)
"/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.hg19.intervals", 1.8, !lowPass, ccs)
)
@ -160,7 +159,8 @@ class pbCalling extends QScript {
val FiltersToIgnore = List("DPFilter", "ABFilter", "ESPStandard", "QualByDepth", "StrandBias", "HomopolymerRun")
// 1.) Call SNPs with UG
class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper {
this.jarFile = gatkJarFile
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)
this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
@ -176,13 +176,13 @@ class pbCalling extends QScript {
else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
// Ridiculous workaround to get pacbio data to run.. never commit this!
this.assume_single_sample_reads = "NA12878"
this.deletions = Some(0.5)
this.mbq = Some(10)
this.deletions = Some(0.5)
this.mbq = Some(10)
}
// 2.) Filter SNPs
class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration with UNIVERSAL_GATK_ARGS {
class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration {
this.jarFile = gatkJarFile
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)
this.scatterCount = 10
@ -194,7 +194,8 @@ class pbCalling extends QScript {
}
// 3.) VQSR part1 Generate Gaussian clusters based on truth sites
class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters with UNIVERSAL_GATK_ARGS {
class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters {
this.jarFile = gatkJarFile
val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
this.reference_sequence = t.reference
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
@ -202,7 +203,10 @@ class pbCalling extends QScript {
this.rodBind :+= RodBind("1kg", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf")
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
if (t.isCCS)
this.use_annotation ++= List("QD", "HaplotypeScore", "HRun")
else
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
this.analysisName = name + "_GVC"
this.intervalsString ++= List(t.intervals)
this.qual = Some(350) // clustering parameters to be updated soon pending new experimentation results
@ -216,7 +220,8 @@ class pbCalling extends QScript {
}
// 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters
class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator with UNIVERSAL_GATK_ARGS {
class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator {
this.jarFile = gatkJarFile
val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
this.reference_sequence = t.reference
if( t.hapmapFile.contains("b37") )
@ -238,6 +243,7 @@ class pbCalling extends QScript {
// 4a.) Choose VQSR tranches based on novel ti/tv
class VariantRecalibratorTiTv(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
this.jarFile = gatkJarFile
this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
this.out = t.titvRecalibratedVCF
this.tranchesFile = t.titvTranchesFile
@ -245,6 +251,7 @@ class pbCalling extends QScript {
// 4b.) Choose VQSR tranches based on sensitivity to truth set
class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
this.jarFile = gatkJarFile
this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY)
this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
this.out = t.tsRecalibratedVCF
@ -255,7 +262,8 @@ class pbCalling extends QScript {
}
// 5.) Variant Cut filter out the variants marked by recalibration to the 99% tranche
class VariantCut(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
class VariantCut(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ApplyVariantCuts {
this.jarFile = gatkJarFile
this.reference_sequence = t.reference
this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF )
this.analysisName = t.name + "_VC"
@ -270,10 +278,11 @@ class pbCalling extends QScript {
}
// 6.) Variant Evaluation based on the sensitivity recalibrated vcf
class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS {
class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval {
this.jarFile = gatkJarFile
val name: String = t.name
this.reference_sequence = t.reference
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
this.rodBind :+= RodBind("comp", "VCF", t.hapmapFile)
this.rodBind :+= RodBind("eval", "VCF", t.cutVCF)
this.analysisName = name + "_VE"
this.intervalsString ++= List(t.intervals)