Aligned reads in a SAM or BAM file typically have a Compact Idiosyncratic Gapped Alignment Report (CIGAR) string that expresses how the read is mapped to the reference genome.
When I first read the CIGAR operator table (above), I was confused by two things:
- the match,
M, operator description, “alignment match (can be a sequence match or mismatch)“, struck me as odd.
- the relationship between the
Xoperators isn’t explained in the spec.
I hope this blog post helps others with the same questions.[Read More]