GATK pre-processing vs firehose

ngreenwaldngreenwald CambridgeMember

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?

Thanks,
Noah.

Best Answer

Answers

Sign In or Register to comment.