I have an output file with predicted variant categories from VEP using VCF file. I am confused with the table it generates. For the same SNP, it has different amino acid change (for example, in the picture below, the p change ranges from p.Thr168Ala to p.Thr747Ala). Is there any criteria to choose on the protein change?
1 answer
Those are all changes on different proteins. I see that you're running VEP on RefSeq. If you're using GRCh38, you can either enable MANE (Merged Annotations between Ncbi and Embl) to get a clearer picture or just annotate against EnsEMBL. What also helps is enabling --canonical option (there is a chackbox for it on the website if annotating against EnsEMBL), or using the --pick-allele option (it is available as a filtering option on the website, choose "one consequence per allele")
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