Is it possible, or a bad idea, to run Ensembl Variant Effect Predictor on a file output from an older version of the same tool?
Long ago, I downloaded some large VCF files, ran them through VEP and then deleted the originals. Now I'd like to run an updated version of VEP on the same files.
Do you think it would work directly, or should I clean out the INFO column and some headers? I don't know if VEP will see existing VCF headers or modify them, or just add more, which would result in conflicting duplicate lines. Also with the INFO column; it might add more data in a confusing way, or replace the existing data.
I could strip the INFO column before running the new VEP, but does it need anything to be left behind? Same for the headers, if I delete them entirely will the newer version of VEP still work?