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  • #1

    MuTect short read preprocessing

    Hi, I am programming to do short read preprocessing for BAM files. I have no idea about how to know if paired-end reads are overlapping and the overlapping region, and the mismatch bases for a read (I know the field MD gives the mismatching position, but I did not understand it. Why it is a string not a numeric array?) Thanks very much for your time.

    Best
    Jing
    Tags: mismatching position, overlapping pe reads
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