Quick question, I googled around but found no answer for it, is there any VEP functionality that allows to know if a variant falls in a repeated region? (I am talking in order to screen for the PM4 ACMG criteria: protein length changes as a result of in-frame deletions/insertions in a non-repeat region or stop-loss variants), or any repeated-regions .bed file available to check it?
Thank you very much in advance for any help!
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written
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cocchi.e89
2 answers
We haven't got any plugins to check repeat regions, I'm afraid. If you have a suitable bed file you can use the custom annotations options, but we don't release bed files of the repeats.
You can make use of the "RepeatMask" track from UCSC, for hg38 you can get it from here. Hope this helps.
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