Question: Restrict ANNOVAR annotation to a list of genes.
0
gravatar for stevenlang123
3.4 years ago by
stevenlang123140
United States
stevenlang123140 wrote:

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?

sequencing next-gen genome • 920 views
ADD COMMENTlink written 3.4 years ago by stevenlang123140

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.

ADD REPLYlink written 3.4 years ago by harold.smith.tarheel4.3k
2
gravatar for Daniel Swan
3.4 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

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..

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Daniel Swan13k
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