[ensembl-dev] Imbalanced variants in BED fromat

[Will McLaren]

Hello,

BED format for variants is not something we explicitly support in Ensembl,
so we're probably not the best place to ask about this.

If this is connected to your other question about using the variants as a
--custom annotation file in the VEP, you'd be better off leaving the file
as a VCF (--custom supports VCF files too).

A quick google unearthed this tool:

https://bedops.readthedocs.org/en/latest/

This might give you some more guidance.

Regards

Will McLaren
Ensembl Variation


On 22 May 2014 15:34, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> I have a question about converting VCF to BED format for unbalanced
> variants:
>
> http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
>
> Is there a consensus as to how the start and end positions should be
> calculated in the BED format?
>
> For instance dbSNP provides files in bed format but found no information
> about that.
>
> Regards,
>
> --
> G.
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140523/7afbe09d/attachment.html>