Can I run VEP on a VCF twice?
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6.0 years ago

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?

VEP VCF • 2.0k views
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If there's uncertainty as to what VEP will do, why not take the first 100 lines of the VCF and just try it?

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6.0 years ago
bruce.moran ▴ 880

Probably good to remove all previous instance of VEP from the VCF. That is what I have done, just for peace of mind. It is a (Perl -ane for me) one-liner, and a quick edit and reheader, so only took a few minutes. Especially if your VCF is large, as VEP takes a reasonable amount of time to complete. Just my 2c though.

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