CLI Overview

The SOPRANO CLI contains utilities for pipeline execution, in addition to several utilities for preparing the necessary data inputs files.

Core executables

• soprano-run
  Execute the SOPRANO pipeline to compute dN/dS, based on a choice of input files and parameter choices.

• soprano-app
  Deploy the SOPRANO user interface to your local browser: run utilities and a light-weight version of the pipeline.

Additional utilities

• soprano-link-vep
  Link a VEP cache containing genome reference files to the SOPRANO data folders.

• soprano-annotate
  Annotate VCF files that can be handled by SOPRANO, describing somatic mutations.

• soprano-get-genome
  Download an ensembl VEP genome reference file from the ensembl FTP server.

• soprano-hla2ip
  Prepare an immunopeptidome file based a discrete choice of HLA; and optional transcript constraints.