Bwa Bwasw Md Tag

Question

[Random]

I mapped some reads to a reference genome using bwa's bwasw option and it seems that the MD tag is never produced. Is there a way to make bwa create this tag for each mapped read?

Alternatively is there way to enforce bwa to output a CIGAR string with "X" and "=" characters (which stand respectively for sequence mismatch and match), instead of the ambiguous M (which stands for both match and mismatch) ?

I'm trying to find out how much of each mapped read mismatched the reference.

Thanks.

Answer 1

[Pierre Lindenbaum]

did you try to use samtools calmd ?

samtools calmd [-EeubSr] [-C capQcoef] <aln.bam> <ref.fasta>

generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Output SAM by default.

[Random]

I hadn't. This seems to solve my problem. Thanks