Hi all,
I have a question about doing the indel realinging and base quality recalibration steps after the initial alignments. Basically, Does it matter the order in which these are done? Can base recalibration be done before the indel realignment? Should it really matter?
Thanks
I have a question about doing the indel realinging and base quality recalibration steps after the initial alignments. Basically, Does it matter the order in which these are done? Can base recalibration be done before the indel realignment? Should it really matter?
Thanks