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!