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Update the DPP and PBPP to use the BQSRv2 walkers

This commit is contained in:
Eric Banks 2012-07-17 13:15:32 -04:00
parent 3a64398d07
commit 17d627b86d
2 changed files with 16 additions and 34 deletions
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25
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -258,8 +258,8 @@ class DataProcessingPipeline extends QScript {
// Accessory files
val targetIntervals = if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY) {globalIntervals} else {swapExt(bam, ".bam", ".intervals")}
val metricsFile = swapExt(bam, ".bam", ".metrics")
val preRecalFile = swapExt(bam, ".bam", ".pre_recal.csv")
val postRecalFile = swapExt(bam, ".bam", ".post_recal.csv")
val preRecalFile = swapExt(bam, ".bam", ".pre_recal.table")
val postRecalFile = swapExt(bam, ".bam", ".post_recal.table")
val preOutPath = swapExt(bam, ".bam", ".pre")
val postOutPath = swapExt(bam, ".bam", ".post")
val preValidateLog = swapExt(bam, ".bam", ".pre.validation")
@ -281,9 +281,7 @@ class DataProcessingPipeline extends QScript {
dedup(cleanedBam, dedupedBam, metricsFile),
cov(dedupedBam, preRecalFile),
recal(dedupedBam, preRecalFile, recalBam),
cov(recalBam, postRecalFile),
analyzeCovariates(preRecalFile, preOutPath),
analyzeCovariates(postRecalFile, postOutPath))
cov(recalBam, postRecalFile))
cohortList :+= recalBam
@ -345,11 +343,11 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".clean"
}
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
case class cov (inBam: File, outRecalFile: File) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs {
this.knownSites ++= qscript.dbSNP
this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam
this.recal_file = outRecalFile
this.out = outRecalFile
if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform
if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals
@ -358,14 +356,14 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outRecalFile + ".covariates"
}
case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs {
this.input_file :+= inBam
this.recal_file = inRecalFile
this.BQSR = inRecalFile
this.disable_indel_quals = true
this.baq = CalculationMode.CALCULATE_AS_NECESSARY
this.out = outBam
if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals
this.no_pg_tag = qscript.testMode
this.scatterCount = nContigs
this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration"
@ -379,13 +377,6 @@ class DataProcessingPipeline extends QScript {
****************************************************************************/
case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates {
this.recal_file = inRecalFile
this.output_dir = outPath.toString
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
}
case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs {
this.input :+= inBam
this.output = outBam

25
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
View File

@ -80,8 +80,8 @@ class PacbioProcessingPipeline extends QScript {
// BAM Steps
val mqBAM: File = swapExt(bamBase, ".bam", ".mq.bam")
val recalFile1: File = swapExt(bamBase, ".bam", ".recal1.csv")
val recalFile2: File = swapExt(bamBase, ".bam", ".recal2.csv")
val recalFile1: File = swapExt(bamBase, ".bam", ".recal1.table")
val recalFile2: File = swapExt(bamBase, ".bam", ".recal2.table")
val recalBam: File = swapExt(bamBase, ".bam", ".recal.bam")
val path1: String = recalBam + ".before"
val path2: String = recalBam + ".after"
@ -102,9 +102,7 @@ class PacbioProcessingPipeline extends QScript {
add(cov(bam, recalFile1, resetQuals),
recal(bam, recalFile1, recalBam),
cov(recalBam, recalFile2, false),
analyzeCovariates(recalFile1, path1),
analyzeCovariates(recalFile2, path2))
cov(recalBam, recalFile2, false))
}
}
@ -162,36 +160,29 @@ class PacbioProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".rg"
}
case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends CountCovariates with CommandLineGATKArgs {
case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs {
if (resetQuals)
this.DBQ = dbq
this.knownSites :+= dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam
this.recal_file = outRecalFile
this.out = outRecalFile
this.analysisName = queueLogDir + outRecalFile + ".covariates"
this.jobName = queueLogDir + outRecalFile + ".covariates"
this.scatterCount = threads
this.read_filter :+= "BadCigar"
}
case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs {
this.DBQ = dbq
this.input_file :+= inBam
this.recal_file = inRecalFile
this.BQSR = inRecalFile
this.out = outBam
this.no_pg_tag = testMode
this.disable_indel_quals = true
this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration"
this.read_filter :+= "BadCigar"
this.scatterCount = threads
}
case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {
this.recal_file = inRecalFile
this.output_dir = outPath
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
}
}