[ensembl-dev] filter_common filter not working

[Duarte Molha]

Great... Thank you for your quick work :)


=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================


On Fri, Aug 23, 2013 at 10:31 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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>>
>
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