VCF to .csv handler catered to specific desired fields
Project description
vcf-handler
This repo is an installable python package and command line tool built for creating .csv files of annotated variants from VCF files. Currently the main process annotates variants with the following information either found within the VCF or pulled from external sources:
- Depth of sequence coverage at the site of variation.
- Number of reads supporting the variant.
- Percentage of reads supporting the variant versus those supporting reference reads.
- Gene ID of the variant, type of variation (substitution, insertion, CNV, etc.) and their effect (missense, silent, intergenic, etc.) using the VEP hgvs API
- The minor allele frequency of the variant if available.
- TBD
This package is publicly installable from PyPI, and can also be executed from the command line w
Developing
This repo uses PDM. Install PDM and then install dependencies with pdm install
.
Running test suite: pdm run test
Running auto-linter: pdm run lint-fix
Releases
This package is published on PyPI. In order to create a new release, bump the version in the pyproject.toml file, create a PR, and merge that change into master. When that change is merged into master, the new version will be automatically recognized and published.
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