Question: Multiple VCF files and VEP
0
gravatar for dav
5.5 years ago by
dav0
Belgium
dav0 wrote:

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.

ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 5.5 years ago by dav0
2

http://en.wikipedia.org/wiki/For_loop

ADD REPLYlink written 5.5 years ago by Pierre Lindenbaum131k

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

ADD REPLYlink written 5.5 years ago by dav0
3
gravatar for Emily_Ensembl
5.5 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

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.

ADD COMMENTlink written 5.5 years ago by Emily_Ensembl21k
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