Hi all and thanks in advance for any help you will kindly provide.
I'm aligning some short sequences against a few databases by means of BWA. I need to recover bot identity and coverage in a fast way at the end of the alignemnet. I read that I can use the M field in CIGAR form SAM and further parameters from SAM to distinguish between match/mismatch. Can you give more precise information on this point?
Is there easy way to modify BWA to have identity and coverage directly (as it is done in DeconSeq, whose code I tried to analyse but with little success)?
Is there any settings for input parameters to BWA to obtain some desired coverage and identity?
Thanks a lot, Giovanna