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Old 12-09-2011, 06:00 AM   #1
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Location: Arlington, VA

Join Date: Apr 2011
Posts: 1
Default 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!!

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Old 12-09-2011, 11:59 AM   #2
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Location: St. Louis

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Posts: 535

It should be easy to write a quick script to filter the genes you want. Is that doable?
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Old 12-09-2011, 12:35 PM   #3
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Location: Germany

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I don't think there is a way. A quick solution is use:

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