GATK pre-processing vs firehose
Hi, we have a bam pre-processing workflow in our lab that I believe was obtained from someone in the GP group at the broad a few years ago. However, it hasn't been updated recently, and it doesnt exactly match up with the current GATK workflow.
BWA ALN | SAMPE | NORM |CLEAN | FIXMATES | add RG | MARKDUP | BQSR |Co-Clean
Specifically, it has a step after BQSR in firehose called co-clean. I was wondering if this is still necessary, since it doesn't seem to appear anywhere on your workflow. It also doesn't appear to have indel realignment?