## Playing with matches and CIGARs

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:

1. the match, M, operator description, “alignment match (can be a sequence match or mismatch)“, struck me as odd.
2. the relationship between the M, = and X operators isn’t explained in the spec.

I hope this blog post helps others with the same questions.

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