Extended CIGAR (sam v.1.4)

[aechchiki]

Hi,

I am using bwa mem to align pacbio reads to a reference. I am wondering if there is a way to obtain an extended CIGAR string (sam v.1.4) in the sam output, as default in bwa aln. I'd like to retrieve details on match/mismatch (X,=) instead of a generic alignment match (M).

Thanks in advance,
Amina

[aechchiki]

Found a tool that can do that a posteriori: SamFixCigar https://github.com/lindenb/jvarkit