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  • Is anyone doing tertiary analysis of their DNASeq data?

    Hello!

    I am new here and just trying to get a sense of what everyone is up to. From reading through pages and pages of this forum, I noticed that I didn't see a lot of threads about the statistical analysis or classification of DNA Seq variants.

    Anyone out there doing this kind of work?



    Cheers,

    Dan

  • #2
    Moved to "General" since this is not a specific question. And yes, many people on the board actively debate the best way to identify true variation from errors arising from sequencing, mapping, etc.

    Comment


    • #3
      Ahh, thank you so much for moving this to the proper place.

      I have experience with collapsing methods for both common and rare variant burden, but not much outside of that for statistical analysis of variant results.

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      • #4
        For determining whether a novel SNP is a potential mutation PolyPhen is pretty good



        Last edited by NextGenSeq; 01-05-2012, 09:55 AM.

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        • #5
          We use several tools to call, classify, assign confidence, and annotate. A good place to start is the GATK website. The GATK calls and integrates variant annotation via SNPEff as well as provides a wealth of info per SNP to help you ascribe a confidence to the call. For comparative analysis we have looked into PLINK/SEQ from Harvard and Goldenhelix (Commercial), and other popular tools for annotation are annovar and Variant Effect predictor from ENSEMBL. In addition to PolyPhen, SIFT is a nice tool/database as well.
          Justin H. Johnson | Twitter: @BioInfo | LinkedIn: http://bit.ly/LIJHJ | EdgeBio

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          • #6
            Justin - thanks for the info. Full disclosure and funny coincidence - I work for Golden Helix!

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