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Published 20 hours ago • verified publisher icon brentp

VEP problems

Open antonkulaga opened this issue 3 years ago • 2 comments

When I try to annotate the results with VEP I get:

WARNING: variant 259 on line 280 is too long to annotate: (78162751)
WARNING: variant 260 on line 281 is too long to annotate: (78180620)
WARNING: variant 398 on line 422 is too long to annotate: (11790044)
...
WARNING: variant 416 on line 442 is too long to annotate: (66354472)
Exiting the program. The input file appears to be unsorted. Please sort by chromosome and by location and re-submit.

Is smoove supposed to be VEP friendly? Are there any additional steps of post-proccessing (or some specific VEP parameters) needed to make it work?

antonkulaga avatar Dec 29 '20 12:12 antonkulaga

Hi, the output should be sorted and indexed. Is there an index along with the file you're annotating? If so, you might want to ask this on the VEP mailing list/issues.

brentp avatar Dec 29 '20 14:12 brentp

I managed to make it work by allowing to process in unsorted order. Regarding the index, I do not remember that vep had a parameter for the index file.

antonkulaga avatar Dec 30 '20 09:12 antonkulaga