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  • dsidote
    Member
    • Aug 2009
    • 23
    #1

    Bioscope clip vs mismatch

    Does anyone know how bioscope decides to Hard Clip vs calling a mismatch ?

    For eg :

    1781_585_1567 0 validated 586867 54 34M1H * 0
    0 ==================================
    IIIIIIIIIIII:EI<FIIDDIIIIIII@EIIII RG:Z:20110112194907919
    NH:i:1 CM:i:0 CQ:Z:<BBAB>A=B?BB4'?2+<@:+:@A@=</<%A4?>?
    CS:Z:T11212021130133312020233301002211032 NM:i:0 MD:Z:34

    Why is the above read are not classified as 35 bp read length with 1 mismatch?

    Thanks!
    Tags: None
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