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Updated Full Processing Pipeline 

* add interleaved fastq option to sam2fastq
    * add optional adapter trimming path
    * add "skip_revert" option to skip reverting the bams (sometimes useful -- hidden parameter)
    * add a walker that reads in one bam file and outputs N bam files, one for each read group in the original bam. This is a very important step in any BAM reprocessing pipeline.

I am using this new pipeline to process the CEU and YRI PCR Free WGS
trios.
This commit is contained in:
Mauricio Carneiro 2013-07-25 17:34:53 -04:00
parent 69e78efeae
commit 765f5450ac
1 changed files with 6 additions and 1 deletions
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7
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
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@ -81,6 +81,9 @@ class SamToFastq extends org.broadinstitute.sting.queue.function.JavaCommandLine
@Argument(shortName = "inpa", fullName = "include_non_primary_alignments", required = false, doc = "If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments.")
var includeNonPrimaryAlignments: Boolean = false
@Argument(shortName = "il", fullName = "interleave", required = false, doc = "Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe which end it came from")
var interleave: Boolean = false
override def inputBams = input
override def outputBam = null
this.sortOrder = null
@ -98,5 +101,7 @@ class SamToFastq extends org.broadinstitute.sting.queue.function.JavaCommandLine
conditional(readOneMaxBasesToWrite >= 0, "READ1_MAX_BASES_TO_WRITE=" + readOneMaxBasesToWrite) +
conditional(readTwoTrim >= 0, "READ2_TRIM=" + readTwoTrim) +
conditional(readTwoMaxBasesToWrite >= 0, "READ2_MAX_BASES_TO_WRITE=" + readTwoMaxBasesToWrite) +
conditional(includeNonPrimaryAlignments, "INCLUDE_NON_PRIMARY_ALIGNMENTS=" + includeNonPrimaryAlignments)
conditional(includeNonPrimaryAlignments, "INCLUDE_NON_PRIMARY_ALIGNMENTS=" + includeNonPrimaryAlignments) +
conditional(interleave, "INTERLEAVE=" + interleave)
}