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  • samtools calmd -e

    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

  • #2
    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.

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