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  • Mendelian inheritance

    I am looking for a sample algorithm or a script for Mendelian inheritance filtering. I have a table of variants and each row represents a unique variation that is shared or not between different members of a large family. I imagine that there should be a meta file I supply with the Mendelian structure information and my script should read that and filter my data based on that meta data. The result should be these variants fit an autosomal recessive inheritance patterns etc. I can provide the expected inheritance pattern in the meta data file as well but the ideal script should be able figure that out as well. Does anyone know anything similar to this before I start melting my brain on this hopefully not reinventing the wheel? Python preferred but a general algorithm is more than OK.
    Thanks

  • #2
    Are you trying to filtering out the Mandelian inconsistencies among the sequences within the family?

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    • #3
      No. I have whole exome sequence data and I want to be able to give a meta data file as the family pedigree that may also contain a suspected mendelian model of inheritance and let the script read that data and apply appropriate analysis to the whole exome variation data accordingly.

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      • #4
        @msincan: Did you have any luck finding/writing that program? I'm interested in something similar.

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        • #5
          Originally posted by erichpowell View Post
          @msincan: Did you have any luck finding/writing that program? I'm interested in something similar.
          I ended up writing it myself. It is a command line python script that runs under Linux/Unix.

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          • #6
            Sounds cool. Do you have any plans to distribute it or share it with others. I would be interested in giving it a try. Let me know.

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