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How do the ftDNA SNP assays and SNP panels “work” at the assay level?

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  • How do the ftDNA SNP assays and SNP panels “work” at the assay level?

    Do people get access to any kind of “raw” data? and How are the assays validated?
    Thanks
    John

  • John-02081
    replied
    I have been looking at my BigY BAM file and I’ve noticed several SNPs that are from Y-chr regions that are repeated elsewhere on the Y-chr (segmental duplications). There are a few (~1%) mismatches between the regions which would usually be enough for the BigY reads (160 bp) to be correctly aligned. However, if left me scratching my head about how a SNP assay could be designed for these locations.

    There are several ways to “design” SNP assays and my first question was concerned with “how do I know that the SNP assays were well designed?”. It can be a difficult task. For example, do the designers have DNA available with the SNP variant for every SNP assay they design?

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  • The_Contemplator
    replied
    No, you don't get any sort of raw data like that. Just a list of SNP names that were tested and you were found positive, negative, or no-call/heterozygous call. If you would like raw data you can look at, you are better off with the Big Y. That one you do get raw data in the form of VCF/BED files and BAM file that you can dig into if you know how.

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  • Jim Barrett
    replied
    I'm not sure if this is what you mean or not. For each SNP tested, either individual SNPs or SNP Pack SNPs you'll be told if you tested or negative for each SNP.

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