From 765f5450ac53a01ccf045dca7e2d977768f0e0cb Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 25 Jul 2013 17:34:53 -0400 Subject: [PATCH] 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. --- .../sting/queue/extensions/picard/SamToFastq.scala | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala index 1f3df2dfa..e09e0c100 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala @@ -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) + } \ No newline at end of file