Variant Effect Predictor plugin for ExAC frequencies
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Entering edit mode
8.1 years ago

Simple question.... Has anyone produced a plugin for adding ExAC allele frequencies to Variant Effect Predictor (VEP) annotation?

VEP variant-annotation ExAC • 4.8k views
5
Entering edit mode
8.1 years ago
EnsemblWill ▴ 560

As the data are available as a VCF file, you can just use the custom annotations feature of the VEP to pull in the sites and any frequency data you want:

curl -O ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz
perl variant_effect_predictor.pl -i example_GRCh37.vcf -cache -custom ExAC.r0.3.sites.vep.vcf.gz,ExAC,vcf,exact,0,AF


Here I've added the AF field (it will appear as ExAC_AF in the VEP output), but you could add any of the fields in the INFO block of the VCF by listing them at the end of the --custom string. See http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html for more info.

You could get a list of fields by doing (this gets the VCF header)

tabix -h ExAC.r0.3.sites.vep.vcf.gz 1:1-1


There's a caveat here in that the VCF carries the per-population allele counts but not the frequencies, so to derive the frequencies you'd need to do a little math(s). It's probably worth writing a plugin to deal with these (and a very simple one it would be too, see the dbNSFP plugin http://www.ensembl.info/ecode/dbnsfp/ for an example of one that uses tabix to retrieve data from a file), but in the short term the above solution should at least get you part of the way.

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Entering edit mode
7.7 years ago

Available for a while, but I forgot to post it: https://github.com/ensembl-variation/VEP_plugins/blob/master/ExAC.pm

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Entering edit mode
8.1 years ago
Emily 23k

Can't see anything obvious on our plugin page, but it doesn't mean that nobody's made it. If anyone has, we'd love to host it.