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Multiple VCF files and VEP

Hello ,

I am using Variant Effect Predictor from Ensembl and I couldnt find notes on using it on multiple vcf files

I have some 1001genome data (A. thaliana) I want to analyze for my target genes , but I couldnt find a way to run it on multiple vcf files provided there.

Is there a way to do it?
Is there another program you would recommend?

I am trying to see deletions/SNPs/CNVs in around 300 genes on around 500 VCF files.

sequence software error snp vep ensembl
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updated by dew • dew • written by dav • dav

I was going to do so , I was thikning of something that would compile the data in one table :)
I solved my problem , thank you very much

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written by dav • dav

1 answer

The VEP will only run on one VCF file at a time. As Pierre suggests, if you want to run it repeatedly on a number of files, you could write a simple programme to run through all the files.

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written by Emily Emily

And then use bcftools to combine the annotated files? Thanks a lot!

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written by dew • dew

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