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Minimal coverage for accurate variant calling according to Illumina FDA submission?

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  • Minimal coverage for accurate variant calling according to Illumina FDA submission?

    Dear all,
    looking up the FDA submission (510K) of the MiSeq Dx platform document, it is stated that the "Recommended minimal coverage per amplicon needed for accurate variant calling (Q(max_gt | poly_site) >=100) is 75x:



    My questions are
    1 - Is there a known rational for this 75x number?
    2 - What does "Q(max_gt | poly_site) >=100" mean?

    Thanks!

  • #2
    If you are not getting accurate calls at 30x coverage over a particular site, 75x won't help you much, because there's some fundamental problem with your methodology. And I think by 75x per amplicon they mean 150x for a human, which seems quite excessive. I imagine that number is designed so that you can screw up a lot of stuff (reduce library complexity by over-amplifying too little input DNA, use exome-capture and an inferior aligner to yield extreme reference-bias, etc) and still have some chance of producing useful data.
    Last edited by Brian Bushnell; 04-30-2015, 08:49 AM.

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    • #3
      Thanks Brian,
      my focus is more on the regulatory point of view though (this is why I was interested by the FDA submission document) so I still need some references/pointers.
      Do you understand this?
      Q(max_gt | poly_site)

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      • #4
        Sorry, no, I have not the slightest idea what that means.

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        • #5
          Originally posted by alunem View Post
          Thanks Brian,
          my focus is more on the regulatory point of view though (this is why I was interested by the FDA submission document) so I still need some references/pointers.
          Do you understand this?
          http://www.illumina.com/documents/pr...provements.pdf

          See page 7 for explanation of Q(max_gt | poly_site) .

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          • #6
            Oh great, thanks.

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