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

[Stuart Watt]

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 <mailto:stuart.watt at uhnresearch.ca>
416-634-8816

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