Additional Commands

To make using pVAC-Seq easier several convenience methods are included in the package.

Download Example Data

usage: pvacseq download_example_data [-h] destination_directory
Required Arguments
 Directory for downloading example data

Install VEP Plugin

usage: pvacseq install_vep_plugin [-h] vep_plugins_path
Required Arguments
 Path to your VEP_plugins directory

List Valid Alleles

usage: pvacseq valid_alleles [-h]
                             [-p {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}]
Optional Arguments
-p, --prediction-algorithm

The epitope prediction algorithms to use

Possible choices: NNalign, NetMHC, NetMHCIIpan, NetMHCcons, NetMHCpan, PickPocket, SMM, SMMPMBEC, SMMalign

Documentation For Configuration Files

usage: pvacseq config_files [-h] {additional_input_file_list}
Required Arguments

The config file type to retrieve more information for

Possible choices: additional_input_file_list