[ensembl-dev] VEP filter for 1000 Genome Frequencies at single base indels

Alex Beesley Alex.Beesley at telethonkids.org.au
Thu Oct 29 12:33:30 GMT 2015


Thanks Will - much appreciated!

Regards
alex

Message: 1
Date: Mon, 26 Oct 2015 13:34:50 +0000
From: Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>
Subject: Re: [ensembl-dev] VEP filter for 100 Genome Frequencies at
single base indwells
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
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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<mailto: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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