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

[Will McLaren]

Hi Alex,

I've committed a fix for this issue to the ensembl-tools repo (on the
release/82 branch); you'll need to re-download it to get the fix, or use
"git pull" if you happened to use git to fetch the repo in the first place.

Regards

Will

On 26 October 2015 at 08:51, Alex Beesley <Alex.Beesley at telethonkids.org.au>
wrote:

> 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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