gatk-3.8/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala

import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.QScript
import org.apache.commons.io.FilenameUtils;
import scala.io.Source._

class MethodsDevelopmentCallingPipeline extends QScript {
  qscript =>

  @Argument(shortName="gatk", doc="gatk jar file", required=true)
  var gatkJarFile: File = _

  @Argument(shortName="outputDir", doc="output directory", required=true)
  var outputDir: String = "./"

  @Argument(shortName="skipCalling", doc="If true, skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)
  var skipCalling: Boolean = false

  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: Option[String], val titvTarget: Double) {
    def name = qscript.outputDir + baseName
    def clusterFile = new File(name + ".clusters")
    def rawVCF = new File(name + ".raw.vcf")
    def filteredVCF = new File(name + ".filtered.vcf")
    def goldStandardName = qscript.outputDir + "goldStandard/" + baseName
    def goldStandardClusterFile = new File(goldStandardName + ".clusters")
  }

  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 hg19 = new File("/seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.fasta")

  //val HiSeq = new Target("NA12878.HiSeq", hg18, "hg18", new File("BAM LIST HERE"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals"), 2.07)
  //val WEx = new Target("NA12878.WEx", hg18, "hg18", new File("BAM LIST HERE"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"), Some("/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)
  //val LowPassN60 = new Target("lowpass.N60", b36, "b36", new File("BAM LIST HERE"), new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals"), 2.3)
  //val LowPassAugust = new Target("ALL.august.v4", hg19, "b37", new File("BAM LIST HERE"), 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"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals"), 2.3)
  val LowPassFIN79Nov = new Target("FIN.nov2010.v4", hg19, "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"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals"), 2.3)
  //val TGPWExFH = new Target("1000G.WEx.FH", hg19, "b37", new File("BAM LIST HERE"), new File("/humgen/gsa-pipeline/PQ7LC/all_batches_v006/Plate_1/SnpCalls/Barcoded_1000G_WEx_Plate_1.cleaned.annotated.handfiltered.vcf"), Some("/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)
  //val TGPWExGdA = new Target("1000G.WEx.GdA", hg19, "b37", new File("BAM LIST HERE"), new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), Some("/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)

  //val targets = List(HiSeq, WEx, LowPassN60, LowPassAugust, TGPWExFH, TGPWExGdA)
  val targets = List(LowPassFIN79Nov)

  def script = {
      def goldStandard = true
      for (target <- targets) {

        if( !skipCalling ) {
          add(new UnifiedGenotyper(target))
          add(new VariantFiltration(target))
          add(new GenerateVariantClusters(target, !goldStandard))
          add(new VariantRecalibratorTiTv(target, !goldStandard))
          add(new VariantRecalibratorNRS(target, !goldStandard))
        }
        
        add(new GenerateVariantClusters(target, goldStandard))
        add(new VariantRecalibratorTiTv(target, goldStandard))
        add(new VariantRecalibratorNRS(target, goldStandard))
      }
  }

  def bai(bam: File) = new File(bam + ".bai")

  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 {
    this.reference_sequence = t.reference
    this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
    if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get)
    this.scatterCount = 50
    this.dcov = Some(50)
    this.input_file :+= t.bamList
    this.out = t.rawVCF
    this.analysisName = t.name + "_UG"
  }

  // 2.) Filter SNPs
  class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration with UNIVERSAL_GATK_ARGS {
    this.reference_sequence = t.reference
    if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get)
    this.scatterCount = 10
    this.variantVCF = t.rawVCF
    this.out = t.filteredVCF
    this.rodBind :+= RodBind("mask", "Bed", "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask." + t.rodName + ".bed")
    this.maskName = "InDel"
    this.filterName ++= List("HARD_TO_VALIDATE")
    this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
    this.analysisName = t.name + "_VF"
  }

  // 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 {
      var name: String = t.name
      if( goldStandard ) { name = t.goldStandardName }
      this.reference_sequence = t.reference
      this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
      this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
      if( goldStandard ) {
        this.rodBind :+= RodBind("input", "VCF", t.goldStandard_VCF)
        this.clusterFile = t.goldStandardClusterFile
      } else {
        this.rodBind :+= RodBind("input", "VCF", t.filteredVCF)
        this.clusterFile = t.clusterFile
      }
      this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
      this.analysisName = name + "_GVC"
      if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get)
      this.qual = Some(300)
      this.std = Some(3.5)
      this.mG = Some(16) // v2 calls
      // ignores
      this.ignoreFilter ++= FiltersToIgnore
  }

  // 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 {
      var name: String = t.name
      if( goldStandard ) { name = t.goldStandardName }

      this.reference_sequence = t.reference
      this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
      this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
      this.rodBind :+= RodBind("truth", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
      if( goldStandard ) {
        this.rodBind :+= RodBind("input", "VCF", t.goldStandard_VCF)
        this.clusterFile = t.goldStandardClusterFile
      } else {
        this.rodBind :+= RodBind("input", "VCF", t.filteredVCF)
        this.clusterFile = t.clusterFile
      }
      this.analysisName = name + "_VR"
      if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get)
      this.ignoreFilter ++= FiltersToIgnore
      this.ignoreFilter ++= List("HARD_TO_VALIDATE")
      this.priorDBSNP = Some(2.0)
      this.priorHapMap = Some(2.0)
      this.target_titv = t.titvTarget
  }

  // 4a.) Choose VQSR tranches based on novel ti/tv
  class VariantRecalibratorTiTv(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
      this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
      this.out = new File(this.name + ".titv.recalibrated.vcf")
      this.tranchesFile = new File(this.name + ".titv.tranches")
  }

  // 4b.) Choose VQSR tranches based on sensitivity to truth set
  class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
      this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY)
      this.tranche ++= List("50", "25", "10", "5", "2", "1", "0.5", "0.1")
      this.out = new File(this.name + ".ts.recalibrated.vcf")
      this.tranchesFile = new File(this.name + ".ts.tranches")
  }
}