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Broad recommends using snpEff to add annotations to VCF files created by GATK. This gives annotations about the effect of a given variant: is it in a coding region? Does it cause a frameshift? What transcripts are impacted? etc. However, snpEff does not provide other annotations you might want, such as 1000 genomes minor allele frequency, SIFT scores, phyloP conservation scores, and so on. I've previously used annovar to get those sorts of things, and that worked well enough, though I did not find it to be especially user-friendly.
So my question is, what other ways have users found of getting this sort of annotation information? I'm interested specifically in human exomes, but I am sure other users reading this Ask the Community post will be interested in answers for other organisms as well. I'm looking for recommendations on what's quick, simple, easy to use, and has been used successfully with VCFs produced by GATK. I'm open to answers in the form of other software tools or sources of raw data that I can easily manipulate on my own.
Thanks in advance.