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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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VEP problems #140

Open antonkulaga opened 3 years ago

antonkulaga commented 3 years ago

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?

brentp commented 3 years ago

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.

antonkulaga commented 3 years ago

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.