[ensembl-dev] regulatory variant with most_severe flag

[Will McLaren]

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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