[ensembl-dev] VEP and lowercase masked reference genome matches

Will McLaren wm2 at ebi.ac.uk
Wed Jan 27 14:51:14 GMT 2016


Hi Stuart,

I don't see why this can't be standard for --check_ref. It hadn't occurred
to me that the reference sequence might be lowercase; if you're using your
own FASTA just for checking then I don't see any harm in comparing them
without a case check.

I've patched a fix to the release/83 branch of ensembl-variation (you can
re-run INSTALL.pl to pick it up); let me know if you're using an older
version and I can patch that too.

Regards

Will McLaren
Ensembl Variation



On 27 January 2016 at 14:38, Stuart Watt <morungos at gmail.com> wrote:

> Hi all
>
> Just come across a strange issue with VEP. We’re re-annotating a whole
> bunch of files with a reference genome that contains some of the lowercase
> masked regions, and we’re getting them filtered out by VEP when using the
> —check-ref warning. This was a surprise as the variant callers were using
> the exact same reference genome but referencing them as uppercase.
>
> Would it be possible to have a kind of non-strict —checkref that is OK
> with lowercase base letters in the reference, so long as it’s the same base
> letter? Or am I doing this totally wrong?
>
> All the best
> Stuart
>> *Stuart Watt, PhD*
> Scientific Research Associate, Princess Margaret Cancer Centre
> MaRS Centre, 101 College Street
> Toronto Medical Discovery Tower, Room 9-302
> Toronto, Ontario, Canada M5G 1L7
> stuart.watt at uhnresearch.ca
> 416-634-8816
>
>
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