Deleted:Getting an error regarding the reference length and coordinates when using Ensembl-vep
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5 months ago
langziv ▴ 20

Hello.
The input that was submitted to Ensembl-vep's API was in the following format:

12  9067664 9116229 A/C -
12  9067664 9116229 A/G -
12  9067664 9116229 A/T -


The command was

ensembl-vep/vep --database -i /input/variants.txt -o output/output.txt


Which yielded the following errors / warnings:

WARNING: Length of reference allele (A length 1) does not match co-ordinates 9067664-9116229 on line 1
WARNING: Length of reference allele (T length 1) does not match co-ordinates 9067664-9116229 on line 4
WARNING: Length of reference allele (C length 1) does not match co-ordinates 9067664-9116229 on line 10
WARNING: Length of reference allele (G length 1) does not match co-ordinates 9067664-9116229 on line 19


I couldn't figure out what these warnings mean. I used vep before and had no issues with the output. I'd be happy to get some insights.
Thanks.

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