Tools for predicting the protein altering effects of the variants from EXON-seq data

Question

[a.james]

Hi

Say I have a lot of variants including INDELS, SNVs, SNPs, etc from the exon-seq dataset. Now, I need to predict whether or not they have any protein-altering effects (for eg. missense, sense), etc.. I need to know whether or not there are any tools available for this which I can use on the command line.

I am aware of ENSEMBLE's online tool for this case. I need to process results from multiple samples.

Any help/suggestion is much appreciated!

[Pierre Lindenbaum]

I am aware of ENSEMBLE's online tool for this case

ensembl's VEP is available as a command line.... https://www.ensembl.org/info/docs/tools/vep/script/index.html

[a.james]

@Pierre Thanks for the link! That's helpful.