[ensembl-dev] regulatory variant with most_severe flag

[Yuan Chen]

ok, thanks

yuan
On 22 May 2014, at 09:12, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Yuan,
> 
> --most_severe doesn't consider regulatory variants, though it probably should. However, this uses a method in the API that is also used in places by the webcode, so I am wary of changing it.
> 
> I'd definitely recommend using --pick if you must have one consequence per variant.
> 
> Will
> 
> 
> On 22 May 2014 05:44, Yuan Chen <yuan at sanger.ac.uk> wrote:
> Hi Will,
> 
> For this variant : 2       11600   .       A       T
> 
> if I use pick with regulatory, I got :
> 2       11600   .       A       T       128     PASS    CSQ=T||MA0139.1|MotifFeature|TF_binding_site_variant|||||||Jaspar_Matrix_CTCF:MA0139.1|18|N|-0.015||-1
> 
> if I use most_severe with regulatory, I got :
> 2       11600   .       A       T       128     PASS    CSQ=||||intergenic_variant||||||||||||
> 
> Do most_severe flag considering regulatory variant ?
> 
> Thanks for your help !
> 
> yuan
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