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  • 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)?

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

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

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      • #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?

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