Commandline Utilities

Updating Your Local Cache

Usage: civicpy update [OPTIONS]

  Updates CIViC content from server and stores to local cache file

Options:
  --soft / --hard         Hard-update from live API (slow) or
                          soft-update from daily precache (fast; default)
  --cache-save-path TEXT  Filepath to save cache to. Default:
                          /home/docs/.civicpy/cache.pkl
  -h, --help              Show this message and exit.

Creating a VCF of CIViC Variants

Usage: civicpy create-vcf [OPTIONS]

  Create a VCF file of CIViC variants

Options:
  -v, --vcf-file-path TEXT        The file path to write the VCF to.
                                  [required]
  -i, --include-status [accepted|submitted|rejected]
                                  Limits the variants and annotations in the
                                  VCF to only the ones that match the given
                                  statuses.               May be specified
                                  more than once.  [required]
  -h, --help                      Show this message and exit.