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

[Stuart Watt]

Amazing support, Will. Many many thanks. 




I admit I haven't dug too deep in this, and it was a surprise for many of us too. 



All the best

Stuart





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On Wed, Jan 27, 2016 at 9:51 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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