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  • agel
    Junior Member
    • Dec 2011
    • 5

    Haplotype Phasing

    I would like to phase whole-genome datasets, some of which are single-end read datasets and some of which are paired-end datasets. Does anyone have experience with this? Should I simply generate a list of SNPs and feed it to existing phasing algorithms? Is there software that can take the raw read data into account (IE SNPs that appear on the same read)?
  • agel
    Junior Member
    • Dec 2011
    • 5

    #2
    Samtools has a phase function, but I can't seem to find how it works. Is it only read-based?

    Comment

    • ymc
      Senior Member
      • Mar 2010
      • 496

      #3
      I want to know too. I only have SNP phasing experience..

      Comment

      • agel
        Junior Member
        • Dec 2011
        • 5

        #4
        I have been unable to determine how samtools phase works. Is there a mailing list or email address of one of the writers I can ask?

        Comment

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