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

Alexey Larionov alexey_larionov at hotmail.com
Mon Jul 28 20:45:51 BST 2014

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



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