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.
Annotating a VCF with data from CIViC Variants¶
Usage: civicpy annotate-vcf [OPTIONS]
Annotate a VCF with information from CIViC
Options:
--input-vcf TEXT A VCF to annotate with information from
CIViC. [required]
--output-vcf TEXT The file path to write the annotated VCF to.
[required]
--reference [NCBI36|GRCh37|GRCh38]
The reference sequence build used to create
the input VCF [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.