[ensembl-dev] VEP: How to get frequency of detected variant instead of the "co-localised MAF"?

Will McLaren wm2 at ebi.ac.uk
Tue Jul 29 13:11:21 BST 2014

Hi Alexey,

I'm afraid it's not easily possible to do as you request, and you're right,
in cases where the 1000 genomes alt allele is actually the most common
allele this can be misleading.

It would, however, be possible to implement a plugin to do the switching
process - if you are reasonably confident in Perl it shouldn't be too big a

It's something we'll look at incorporating into the core VEP code in future.


Will McLaren
Ensembl Variation

On 28 July 2014 20:45, Alexey Larionov <alexey_larionov at hotmail.com> wrote:

> VEP provides “co-localised MAF” for the detected variants.  This may not
> be sufficient to estimate the 1k frequency of the detected variant, for
> instance if there are multiple alleles at this location.
> Furthermore, VEP provides “--filter_common” option to exclude variants
> co-located with existing common allele (MAF > 1%).  This is commonly
> interpreted as excluding the common variants.  Unfortunately the above
> interpretation is completely wrong for many hundreds of variants, where the
> minor (very rare) allele is incorporated in reference genome (e.g.
> rs6672356, rs4274008, rs7545802, rs198400, rs1763642, rs6429745 etc).  On
> my experience, this this “co-localised MAF” clause is very confusing for
> many biologists, who merely want excluding the common variants.
> Is it possible to use VEP for retrieving 1k allele frequency for the
> DETECTED variant, in addition/instead to the frequency co-localised minor
> allele?
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