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  • karl_s
    Junior Member
    • Dec 2013
    • 9
    #1

    Converting variant alleles back to reference in an alignment

    Hi All,
    I am trying to create a "normal reference" BAM file from a set of BAM files that are contaminated with tumor. I was thinking to merge the BAM files, call variants, and then go back and edit the reads - replacing the mutant alleles with reference. Maybe this is crazy, but I want to create a normal reference from these patients, so that I can use it to call somatic variants on the same patients post-relapse samples, for example, with MuTect.
    Any ideas?
    thanks
    Tags: None
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