[ensembl-dev] VEP VCF custom annotation for gnomad coverage

[Nikolas Pontikos]

Dear Developers,

I want to add custom annotation to VEP.
Specifically I want to add the gnomad coverage downloaded from here:
http://gnomad.broadinstitute.org/downloads

This is important because a colleague pointed out that, at the moment, it
not possible to distinguish between not covered and covered but zero allele
freq in gnomad.

My first attempt was to convert to VCF with REF and ALT set to 'X' as they
should not be needed by tabix.  However this doesn't work.

Does VEP use the REF and ALT in the matching then?  I thought it was simply
using positions with tabix.

For now, I have converted the per position coverage files to bed instead
and that seems to work ok, although the output is not as nice.

Many Thanks,

Nikolas.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170627/d3ac48c5/attachment.html>