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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>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. <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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. <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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? <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>