{"id":48413486,"url":"https://github.com/sgkit-dev/vcztools","last_synced_at":"2026-04-06T06:34:39.295Z","repository":{"id":246228460,"uuid":"820477598","full_name":"sgkit-dev/vcztools","owner":"sgkit-dev","description":"Partial reimplementation of bcftools for VCF 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Downloads](https://static.pepy.tech/badge/vcztools)](https://pepy.tech/projects/vcztools)\n\n# vcztools\nPartial reimplementation of bcftools for [VCF Zarr](https://github.com/sgkit-dev/vcf-zarr-spec/)\n\nPlease see the [preprint](https://www.biorxiv.org/content/10.1101/2024.06.11.598241) for more information.\n\n\n## Installation\n\n```\npython3 -m pip install vcztools\n```\n\n## Usage\n\n```\nvcztools view \u003cpath.vcz\u003e\n```\nor\n```\npython -m vcztools view \u003cpath.vcz\u003e\n```\nshould be equivalent to running\n```\nbcftools view \u003cpath.vcf.gz\u003e\n```\n\nSee the [bio2zarr](https://sgkit-dev.github.io/bio2zarr/) project for help in\nconverting VCF files to Zarr.\n\n## Goals\n\nVcztools aims to be a drop-in replacement for a subset of bcftools functionality.\nCurrently supported are the ``view``, ``query`` and ``index -s/-n`` commands.\n\nWe aim for 100% compatibility so if you notice a difference between the output of\nvcztools and bcftools please do open an issue.\n\n## Cloud stores\n\nVcztools can read vcz files from cloud stores using [fsspec](https://filesystem-spec.readthedocs.io/en/latest/).\n\nFor example, to read from Amazon S3, first install the `s3fs` fsspec library:\n\n```\npython3 -m pip install s3fs\n```\n\nThen provide your AWS credentials as described in the [`s3fs` documentation](https://s3fs.readthedocs.io/en/latest/#credentials), for example by setting environment variables:\n\n```\nexport AWS_ACCESS_KEY_ID=...\nexport AWS_SECRET_ACCESS_KEY=...\n```\n\nYou can then run vcztools using an `s3://` URL:\n\n```\npython -m vcztools view s3://\u003cbucket-name\u003e/path/to.vcz\n```\n\n## Development\n\nVcztools is under active development and contributions are warmly welcomed. Please\nsee the project on [GitHub](https://github.com/sgkit-dev/vcztools).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsgkit-dev%2Fvcztools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsgkit-dev%2Fvcztools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsgkit-dev%2Fvcztools/lists"}