Mauricio Carneiro 765f5450ac 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.		2013-08-13 23:35:32 -04:00
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qscript/org/broadinstitute/sting/queue/qscripts	Now that we don't generate dict and fai files, the resource script needs to copy them to the bundle.	2013-05-02 15:18:13 -04:00
src/org/broadinstitute/sting/queue	Updated Full Processing Pipeline	2013-08-13 23:35:32 -04:00
test/org/broadinstitute/sting/queue	Disable RetryMemoryLimit pipeline test	2013-07-03 13:38:28 -04:00