[ensembl-dev] VEP filter for 100 Genome Frequencies at single base indwells

[Alex Beesley]

Hi team - I have been using the VEP filter script to filter variants based on 1000 Genome frequencies (--filter "GMAF not > 0.01"), but this doesn't seem to recognise frequencies for single base indels.
For example, the following is a high frequency indel for which the base is not indicated because it is a deletion. But one would still want to filter it out.

rs142545439
GMAF
 -:0.3706

Unfortunately the VEP filter does not seem to recognise the format of these frequencies and refuses to cooperate with any of the operators (e.g.  < or >). The same applies to all the other 1000Genome population frequencies. Help!

Thanks in advance
Alex



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