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Phasing Programs for CGI whole genomes

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  • Phasing Programs for CGI whole genomes

    Hi everyone,

    I have a simple question, followed by more info below if needed:

    What have you been using for phasing your CGI data?

    ------------
    Background:

    I have a fairly large cohort of Whole Genomes sequenced by CGI.

    We have ~90 African Americans and ~30 European Americans.

    There are a lot of programs that can phase NGS data, but I was wondering if the community of people working specifically with CGI-sequenced data have converged on either:

    1. a best software for this, especially if one has the luxury of a larger cohort
    2. a way to do this for CGI BAM files, since they are slightly different

    Am I correct in assuming that most software programs will not handle CGI BAMs correctly? If this is the case, can a VCF be used instead? Is there anything like acceptance of a best software here?

    Thank you!

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