Is it possible to annotate a file for the human genome using the command line without using an amino acid sequence

Question

[kamanovae]

Hi,

I need to run Provean on the server, but I only have a vcd file without an amino acid sequence. The browser version provides the ability to annotate nucleotide variants for the human genome (http://provean.jcvi.org/genome_submit_2.php?species=human).

Can I run the Provean in the same way in the command line?

The use of the command line is required in this case.

Thanks

Answer 1

[GenoMax]

As shown in the README, provean should run on the command line. Download and follow install directions. This program requires old version of BLAST and other dependencies. It was last updated in 2015 so keep that in mind.

You may want to use VEP or snpEff or one of the currently supported annotation programs.

[kamanovae]

Thanks for the answer! I have already installed the program, but it doesn't work only based on the vcd file and doesn't give any error. Is there a way to run the PROVEAN Genome Variants outside the browser?