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BWA mem -M option

bwa mem has an -M flag that will:

Mark shorter split hits as secondary (for Picard compatibility).

However, my guess is Picard has since been updated and this is no longer required. Should bwa mem be run with or without the -M flag assuming we are using relatively up to date software?

Best Answer


  • danielecookdanielecook Member
    edited December 5

    Thank you very much

  • danielecookdanielecook Member
    edited December 5

    One other question @bhanuGandham. Would using the -M flag interfere with MarkDuplicates functionality in terms of marking duplicates?


  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @danielecook

    I do not believe that the-M option interferes with MarkDuplicates functionality. -M option is in fact used to facilitate the working of it. MarkDuplicates does not work with split alignments and hence -M option to flag them as secondary.
    Hope this helps.


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