Implementation of bcftools for VCF Zarr

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  • License: Apache Software License (Apache License)
  • Author: sgkit Developers
  • Requires: Python >=3.10
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vcztools

Partial reimplementation of bcftools for VCF Zarr

Please see the preprint for more information.

Installation

python3 -m pip install vcztools

Usage

vcztools view <path.vcz>

or

python -m vcztools view <path.vcz>

should be equivalent to running

bcftools view <path.vcf.gz>

See the bio2zarr project for help in converting VCF files to Zarr.

Goals

Vcztools aims to be a drop-in replacement for a subset of bcftools functionality. Currently supported are the view, query and index -s/-n commands.

We aim for 100% compatibility so if you notice a difference between the output of vcztools and bcftools please do open an issue.

Cloud stores

Vcztools can read vcz files from cloud stores using fsspec.

For example, to read from Amazon S3, first install the s3fs fsspec library:

python3 -m pip install s3fs

Then provide your AWS credentials as described in the s3fs documentation, for example by setting environment variables:

export AWS_ACCESS_KEY_ID=...
export AWS_SECRET_ACCESS_KEY=...

You can then run vcztools using an s3:// URL:

python -m vcztools view s3://<bucket-name>/path/to.vcz

Development

Vcztools is under active development and contributions are warmly welcomed. Please see the project on GitHub.

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  • License: Apache Software License (Apache License)
  • Author: sgkit Developers
  • Requires: Python >=3.10
  • Provides-Extra: dev
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This version

0.1.0

0.0.2

0.0.1

0.0.1a3 pre-release

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