VEP repeated region flag

Question

[cocchi.e89]

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!

Answer 1

[Emily]

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.

Answer 2

[Vivek Todur]

You can make use of the "RepeatMask" track from UCSC, for hg38 you can get it from here. Hope this helps.