samtools calmd -e

[nergaon]

Hi
I was using the samtools calmd –e command and changed all the basses that are identical to the reference to '='.
What can be done if I want to have the bases back?
Thanks

[Richard Finney]

The -e option converts base matches to '='. Run samtools calmd without -e and you won't have them in the first place. If you're stuck with a bam with this favor already done for you, then a custom repair program is in order. I'm unaware of any existing implementations ... but this is the place to ask.