[ensembl-dev] VEP custom annotation using BED

[Will McLaren]

Your understanding is correct.

For unbalanced variants, there is no difference; any feature from the BED
that overlaps any part of the coordinates representing the input variant
should be reported.

In the odd case of insertions, where in Ensembl/VEP we represent this as
start = end + 1 (where the base(s) are inserted between those two
coordinates), the inserted base must fall _within_ the BED feature to be
reported. Here's an example

BED:

chr1    10      20      feature1

Input variants:

1    20    21    AG/-  # deletion, feature1 reported
1    21    20    -/T     # insertion, feature1 NOT reported
1    20    19    -/T     # insertion, feature1 reported

Hope that helps

Will McLaren
Ensembl Variation


On 22 May 2014 19:21, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> When adding cusom annotations in VEP using a bed file as described here:
>
> http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html
>
> does the annotation type 'overlap' cause the reporting of all overlapping
> regions in the BED file for a given input variant? How is the overlap
> assessed for imbalanced variants?
>
> Thanks,
>
> --
> G.
>
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