ANNOVAR question

[prayingmantis]

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

[Heisman]

It should be easy to write a quick script to filter the genes you want. Is that doable?

[Ooinp]

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

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