This question pertains to the BWA uniq option in the [Set Optional Parameters window]. What are the differences between the four possible choices for “Please choose uniq mode.”?

Last updated:2015.4.28.
  1. Do not remove any read.
    Do not take any steps to ensure uniqueness.
  2. Retain pairs when both reads mapped uniquely or one of reads mapped uniquely, and Discard other pairs.
    Retain a pair if either one or both of the two reads mapped uniquely. (The pair will be discarded if both reads yielded multiple hits.)
  3. Retain pairs when both reads mapped uniquely, and Discard other pairs.
    Retain a pair only if both reads mapped uniquely. (The pair will be discarded if either or both of the reads yielded multiple hits.)
  4. Retain uniquely mapped reads and discard multiply mapped reads.
    Retain only uniquely mapped reads irrespective of pairing.

    The optimal setting for this option depends on the circumstances, but option 3 is the most stringent, option 2 is the most lenient, and option 4 is somewhat intermediate between these two options.

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