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.
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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.
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