Using CIGAR match operators

Question

[mikhail.shugay]

SAM format specification tells that M (alignment match) CIGAR operator can be used instead of the = (sequence match) and X (sequence mismatch) operators. Now I've got interested in how using the M operator affects the performance and functionality of downstream processing tools (say, GATK) and alignment viewer software (say, IGV).

I've seen the relevant question, Should We Attempt To Redefine The Cigar String In Sam/Bam Format?, but I'm still quite confused whether any of commonly used tools are optimized regarding those operators. It would be great if someone can share his experience.

Answer 1

[Brian Bushnell]

All of my tools are optimized for X and =. The only time I use the M symbol is for an N or other non-ACGT character.