Restrict ANNOVAR annotation to a list of genes.

Question

[stevenlang123]

I have a list of ~100 genes and around 100 VCF files, I wish to run ANNOVAR to get functional prediction like SIFT, polyphen etc. But I only want to collect this information a a predefined list of ~100 genes (not the whole VCF). What is the fastest way to do this without directly editing the VCF itself?

[harold.smith.tarheel]

Alternatively, you can edit the ANNOVAR annotation file so that it contains only the 100 genes of interest. Then the exonic output will contain variants for that gene set.

Answer 1

[User 59]

If you really want an Annovar specific solution:

http://annovar.openbioinformatics.org/en/latest/user-guide/region/#identifying-variants-in-regions-specified-in-bed-files

But you could intersect the VCF file with the bed file and annotate the results.

Or annotate everything and parse out the genes you're interested in..