To produce SAM output in SAM 1.4 format (specifically, to represent sequence mismatches and matches with 'X' and '=' instead of 'M' in CIGAR) using cigarUseSeqMatch - pb-cdunn/blasr GitHub Wiki

In order to produce SAM output in SAM 1.4 format, specifically, to represent sequence mismatches and matches with 'X' and '=' instead of 'M' in CIGAR string, please use tag -cigarUseSeqMatch.

./blasr reads.fa ref.fa -sam -out out.sam -cigarUseSeqMatch