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  • BWA and gaps

    In the BWA manual, I see options referring to "gap opens" and "gap extensions". What does this mean? Also, for a typical user who wants to identify SNPs, indels, etc. in a data set, is there are the default options with regard to gaps likely pretty optimal? I realize that you can always tweak stuff, but I started wondering more about messing around with gap options when I saw a paper refer to "gap-enabled BWA". This made me concerned that without messing around with these options, my BWA was not "gap-enabled", but as far as I can tell, the default options are good for dealing with gaps.

    Thanks.

    Eric

  • #2
    Originally posted by efoss View Post
    In the BWA manual, I see options referring to "gap opens" and "gap extensions". What does this mean? Also, for a typical user who wants to identify SNPs, indels, etc. in a data set, is there are the default options with regard to gaps likely pretty optimal? I realize that you can always tweak stuff, but I started wondering more about messing around with gap options when I saw a paper refer to "gap-enabled BWA". This made me concerned that without messing around with these options, my BWA was not "gap-enabled", but as far as I can tell, the default options are good for dealing with gaps.

    Thanks.

    Eric
    It is enabled by default in BWA, but gap-enabled distinguishes it from similar pieces of software which aren't gap enabled, or even gap capable, which of course isn't a selling point so much as being gap enabled.

    Comment


    • #3
      Originally posted by rskr View Post
      It is enabled by default in BWA, but gap-enabled distinguishes it from similar pieces of software which aren't gap enabled, or even gap capable, which of course isn't a selling point so much as being gap enabled.
      Thanks. That makes sense.

      And to the other part of my question: What are "gap opens" and "gap extensions"?

      Thanks.

      Eric

      Comment


      • #4
        the penalty of of a contiguous indel of length L is scored by F(L) = O + L*E, where O is the gap open penalty and E is the gap penalty. The first gap in the indel is scored (O+E), while the following gap (extensions) have score E. I would recommend buying an intro bioinformatics book like Jones and Pevzner.

        Comment


        • #5
          Originally posted by nilshomer View Post
          the penalty of of a contiguous indel of length L is scored by F(L) = O + L*E, where O is the gap open penalty and E is the gap penalty. The first gap in the indel is scored (O+E), while the following gap (extensions) have score E. I would recommend buying an intro bioinformatics book like Jones and Pevzner.
          Thanks, Nils Homer. I just put in an order for your suggestion on Amazon.

          Eric

          Comment


          • #6
            By the way, what is the difference with SW algorithm?

            Comment

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