dnbaker
commented
9 years ago As of now, we have decided to go with the FP:i:[01] tag, particularly because it's easier to add this tag with bwa mem -C than to modify the flag field.
Closed dnbaker closed 9 years ago
dnbaker
commented
9 years ago As of now, we have decided to go with the FP:i:[01] tag, particularly because it's easier to add this tag with bwa mem -C than to modify the flag field.
Since FM < [small positive integer] reads are full of errors and killing our estimation of a variety of things, make decisions as to how to set the 512 flag in samtools.