[ensembl-dev] filter_common filter not working

Duarte Molha duartemolha at gmail.com
Thu Aug 22 16:13:41 BST 2013

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
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

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.

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