Restrict ANNOVAR annotation to a list of genes.
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?
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stevenlang123
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If you really want an Annovar specific solution:
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..
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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.