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  • prayingmantis
    Junior Member
    • Apr 2011
    • 1
    #1

    ANNOVAR question

    Hi everyone,

    Have a question regarding workflow in ANNOVAR. I would like to have the genelist that auto_annovar generates be annotated with the information that is output with the summarize to CSV script. It's nice to have a list of candidate genes that annovar picks out in a gene list, but then it seems cumbersome to have to go back to the summary csv and inspect each SNP for quality, polyphen, etc.

    So my question: is there anyway to have the final genelist generated by ANNOVAR annotated?

    Thanks so much for any help!!

    -Chris
    Tags: None
  • Heisman
    Senior Member
    • Dec 2010
    • 534
    #2
    It should be easy to write a quick script to filter the genes you want. Is that doable?

    Comment

    • Ooinp
      Junior Member
      • May 2011
      • 6
      #3
      I don't think there is a way. A quick solution is use:

      grep -wf [genelist] [summary file] > [outputfile]

      Comment

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