BLASR BAMs and new BWA parameters
*Added the functions to turn a BLASR generated BAM file into a usable BAM file. *Modified the bwa parameters according to test results from NA12878 pb2k dataset.
This commit is contained in:
Mauricio Carneiro
parent
e3f5d7067a
commit
16caca0822
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@ -4,9 +4,9 @@ import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.util.QScriptUtils
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import net.sf.samtools.SAMFileHeader.SortOrder
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import org.broadinstitute.sting.queue.extensions.picard.{SortSam, AddOrReplaceReadGroups}
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import org.broadinstitute.sting.utils.exceptions.UserException
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import org.broadinstitute.sting.commandline.Hidden
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import org.broadinstitute.sting.queue.extensions.picard.{ReorderSam, SortSam, AddOrReplaceReadGroups}
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/**
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* Created by IntelliJ IDEA.
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@ -16,7 +16,7 @@ import org.broadinstitute.sting.commandline.Hidden
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*/
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class RecalibrateBaseQualities extends QScript {
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class PacbioProcessingPipeline extends QScript {
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@Input(doc="input FASTA/FASTQ/BAM file - or list of FASTA/FASTQ/BAM files. ", shortName="i", required=true)
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var input: File = _
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@ -39,13 +39,16 @@ class RecalibrateBaseQualities extends QScript {
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@Input(doc="The path to the binary of bwa to align fasta/fastq files", fullName="path_to_bwa", shortName="bwa", required=false)
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var bwaPath: File = _
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@Input(doc="Input is a BLASR generated BAM file", shortName = "blasr", fullName="blasr_bam", required=false)
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var BLASR_BAM: Boolean = false
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@Hidden
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@Input(doc="The default base qualities to use before recalibration. Default is Q20 (should be good for every dataset)." , shortName = "dbq", required=false)
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var dbq: Int = 20
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@Hidden
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@Input(shortName="bwastring", required=false)
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var bwastring: String = ""
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val queueLogDir: String = ".qlog/"
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@ -57,8 +60,6 @@ class RecalibrateBaseQualities extends QScript {
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var USE_BWA: Boolean = false
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println("DEBUG: processing " + file + "\nDEBUG: name -- " + file.getName)
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if (file.endsWith(".fasta") || file.endsWith(".fq")) {
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if (bwaPath == null) {
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throw new UserException("You provided a fasta/fastq file but didn't provide the path for BWA");
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@ -69,28 +70,34 @@ class RecalibrateBaseQualities extends QScript {
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// FASTA -> BAM steps
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val alignedSam: File = file.getName + ".aligned.sam"
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val sortedBam: File = swapExt(alignedSam, ".sam", ".bam")
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val qualBam: File = swapExt(sortedBam, ".bam", ".q.bam")
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val rgBam: File = swapExt(file, ".bam", ".rg.bam")
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val bamBase = if (USE_BWA) {rgBam} else {file}
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// BAM Steps
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val mqBAM: File = swapExt(bamBase, ".bam", ".mq.bam")
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val recalFile1: File = swapExt(bamBase, ".bam", ".recal1.csv")
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val recalFile2: File = swapExt(bamBase, ".bam", ".recal2.csv")
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val recalBam: File = swapExt(bamBase, ".bam", ".recal.bam")
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val path1: String = recalBam + ".before"
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val path2: String = recalBam + ".after"
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if (USE_BWA) {
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add(align(file, alignedSam),
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sortSam(alignedSam, sortedBam),
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addQuals(sortedBam, qualBam, dbq),
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addReadGroup(qualBam, rgBam, sample))
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addReadGroup(sortedBam, rgBam, sample))
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}
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add(cov(bamBase, recalFile1),
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recal(bamBase, recalFile1, recalBam),
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else if (BLASR_BAM) {
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val reorderedBAM = swapExt(bamBase, ".bam", ".reordered.bam")
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add(reorder(bamBase, reorderedBAM),
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changeMQ(reorderedBAM, mqBAM))
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}
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val bam = if (BLASR_BAM) {mqBAM} else {bamBase}
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add(cov(bam, recalFile1),
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recal(bam, recalFile1, recalBam),
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cov(recalBam, recalFile2),
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analyzeCovariates(recalFile1, path1),
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analyzeCovariates(recalFile2, path2))
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@ -110,13 +117,13 @@ class RecalibrateBaseQualities extends QScript {
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case class align(@Input inFastq: File, @Output outSam: File) extends ExternalCommonArgs {
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def commandLine = bwaPath + " bwasw -b5 -q2 -r1 -z10 -t8 " + reference + " " + inFastq + " > " + outSam
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def commandLine = bwaPath + " bwasw -b5 -q2 -r1 -z20 -t16 " + reference + " " + inFastq + " > " + outSam
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this.memoryLimit = 8
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this.analysisName = queueLogDir + outSam + ".bwa_sam_se"
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this.jobName = queueLogDir + outSam + ".bwa_sam_se"
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}
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case class sortSam (@Input inSam: File, @Output outBam: File) extends SortSam with ExternalCommonArgs {
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@Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai")
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case class sortSam (inSam: File, outBam: File) extends SortSam with ExternalCommonArgs {
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this.input = List(inSam)
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this.output = outBam
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this.sortOrder = SortOrder.coordinate
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@ -124,10 +131,16 @@ class RecalibrateBaseQualities extends QScript {
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this.jobName = queueLogDir + outBam + ".sortSam"
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}
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case class addQuals(inBam: File, outBam: File, qual: Int) extends PrintReads with CommandLineGATKArgs {
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case class reorder (inSam: File, outSam: File) extends ReorderSam with ExternalCommonArgs {
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this.input = List(inSam)
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this.output = outSam
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this.sortReference = reference
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}
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case class changeMQ(inBam: File, outBam: File) extends PrintReads with CommandLineGATKArgs {
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this.input_file :+= inBam
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this.out = outBam
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this.DBQ = qual
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this.read_filter :+= "ReassignMappingQuality"
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}
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case class addReadGroup (inBam: File, outBam: File, sample: String) extends AddOrReplaceReadGroups with ExternalCommonArgs {
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@ -145,6 +158,7 @@ class RecalibrateBaseQualities extends QScript {
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}
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case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
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this.DBQ = dbq
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this.knownSites :+= dbSNP
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this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
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this.input_file :+= inBam
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@ -155,6 +169,7 @@ class RecalibrateBaseQualities extends QScript {
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}
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case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
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this.DBQ = dbq
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this.input_file :+= inBam
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this.recal_file = inRecalFile
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this.out = outBam
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@ -11,7 +11,7 @@ import java.io.File
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*/
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class ReorderSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction {
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analysisName = "ReorderSam"
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javaMainClass = "net.sf.picard.sam.SortSam"
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javaMainClass = "net.sf.picard.sam.ReorderSam"
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@Input(doc="Input file (bam or sam) to extract reads from.", shortName = "input", fullName = "input_bam_files", required = true)
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var input: List[File] = Nil
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@ -22,27 +22,27 @@ class ReorderSam extends org.broadinstitute.sting.queue.function.JavaCommandLine
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@Output(doc="The output bam index", shortName = "out_index", fullName = "output_bam_index_file", required = false)
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var outputIndex: File = _
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@Argument(doc="Reference sequence to reorder reads to match.", shortName = "input", fullName = "input_bam_files", required = true)
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var reference: File = _
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@Argument(doc="Reference sequence to reorder reads to match.", shortName = "ref", fullName = "sort_reference", required = true)
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var sortReference: File = _
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@Argument(doc="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs. By default, this tool requires a corresponding contig in the new reference for each read contig.", shortName = "aic", fullName = "allow_incomplete_concordance", required = false)
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var ALLOW_INCOMPLETE_DICT_CONCORDANCE: Boolean = false
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var ALLOW_INCOMPLETE_DICT_CONCORDANCE: Boolean = _
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@Argument(doc="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length. Highly dangerous, only use if you know what you are doing.", shortName = "acld", fullName = "allow_contig_length_discordance", required = false)
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var ALLOW_CONTIG_LENGTH_DISCORDANCE: Boolean = false
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var ALLOW_CONTIG_LENGTH_DISCORDANCE: Boolean = _
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override def freezeFieldValues() {
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super.freezeFieldValues()
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if (outputIndex == null && output != null && output.toString.endsWith(".bam"))
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if (outputIndex == null && output != null)
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outputIndex = new File(output.getName.stripSuffix(".bam") + ".bai")
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}
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override def inputBams = input
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override def outputBam = output
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this.createIndex = Some(outputIndex != null)
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this.createIndex = Some(true)
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this.sortOrder = null
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override def commandLine = super.commandLine +
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" REFERENCE=" + reference +
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conditionalParameter (ALLOW_INCOMPLETE_DICT_CONCORDANCE, " ALLOW_INCOMPLETE_DICT_CONCORDANCE=true")
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conditionalParameter (ALLOW_CONTIG_LENGTH_DISCORDANCE, " ALLOW_CONTIG_LENGTH_DISCORDANCE=true")
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" REFERENCE=" + sortReference +
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optional(" ALLOW_INCOMPLETE_DICT_CONCORDANCE=", ALLOW_INCOMPLETE_DICT_CONCORDANCE)
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optional(" ALLOW_CONTIG_LENGTH_DISCORDANCE=", ALLOW_CONTIG_LENGTH_DISCORDANCE)
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}
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