https://github.com/griffithlab/civic2clinvar

extraction of CIViC variants into the clinvar submission format
https://github.com/griffithlab/civic2clinvar

civic

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extraction of CIViC variants into the clinvar submission format

• Host: GitHub
• URL: https://github.com/griffithlab/civic2clinvar
• Owner: griffithlab
• License: mit
• Created: 2018-04-15T16:02:57.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2019-04-02T01:43:41.000Z (over 5 years ago)
• Last Synced: 2024-10-31T19:55:57.347Z (14 days ago)
• Topics: civic
• Language: Python
• Size: 11.7 KB
• Stars: 1
• Watchers: 14
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# civic2clinvar

`civic2clinvar` is a python-based command line utility for extracting [CIViC](https://civicdb.org) assertions and translating them into ClinVar records.

## Installation

`$ pip install civic2clinvar`

## Usage

```

$ civic2clinvar --help

Usage: civic2clinvar [OPTIONS] ASSERTION_IDS

  This command generates a ClinVar-formatted csv file from a specified set

  of CIViC assertions.

  ASSERTION_IDS are a comma-separated list of assertions, and accepts

  integer ranges. Example usage:

  civic2clinvar 1,3-5

  The above command outputs a ClinVar submission form describing CIViC

  assertions 1, 3, 4, and 5 to clinvar.csv (the default output file). Output

  destination may be controlled with the --out option, detailed below.

  CIViC assertions that are rejected or pending are skipped.

Options:

  --aid-file FILENAME  Optional file of newline-separated assertion IDs. This

                       option is mutually exclusive with the ASSERTION_IDS

                       argument.

  -o, --out FILENAME   Output file (default: clinvar.csv), use '-' for STDOUT

  --help               Show this message and exit.

```