[ensembl-dev] filter_common filter not working

[Will McLaren]

Thanks Duarte, the VEP was being caught out by having multiple co-located
variants.

This is fixed on CVS now.

Will


On 22 August 2013 16:13, Duarte Molha <duartemolha at gmail.com> wrote:

> Dear developers...
>
> I was wondering if you could let me know what is going on with a
> annotation run I have done.
>
> here is the VCF line I am annotating:
>
> 22           20780091             .               C
> G             37059.72              PASS
> AC=2;AF=1.000;AN=2;BaseQRankSum=0.179;DP=1208;Dels=0.00;FS=22.647;HRun=6;HaplotypeScore=1.4039;InbreedingCoeff=-0.0011;MQ0=0;MQ=52.10;MQRankSum=5.421;QD=30.68;ReadPosRankSum=5.470;SB=-14651.30;set=variant2
> GT:AD:DP:GQ:PL              1/1:0,47:47:99:1482,126,0
>
> and here is one of the my annotation output lines:
>
> 22_20780091_C/G           22:20780091       rs759610,rs77189880
> G             HOM     ENSG00000244486
> ENST00000266214                Transcript            synonymous_variant
> C:0.1383
>
> as you can see from this line the gmaf frequency being reported is
> C:0.1383.
>
> However I was using the filter_common flag so this variation should have
> been disregarded because the gmaf is above 0.01.
>
> Can you explain to be if I am doing something wrong here?
>
> Your help is much appreciated.
>
> Duarte
>
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