[ensembl-dev] how to force VEP to only return unique Gene IDs per variant

Wibo Pipping wibo at thehyve.nl
Thu Jun 25 14:49:52 BST 2015


Hi Ensembl team,

I have annotated a VCF file with entrez gene IDs using VEP 79. (command
used: perl ~/variant_effect_predictor.pl -i inputfile.vcf --cache --refseq
--vcf --offline

The output I get back has some weird results. Basically it is doing this:

GID=6790,6790,6790,6790,6790,6790,6790,6790,6790;GS=AURKA,AURKA,AURKA,AURKA,AURKA,AURKA,AURKA,AURKA,AURKA.

This is for one variant. Is there a way I can tell it to not report
duplicates in the same variant?

Thank you!


Regards,

Wibo Pipping
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