Introduction#
vcztools provides
bcftools-compatible
querying and format conversion for VCF Zarr (VCZ).
Please see the GigaScience paper
and the specification repo
for more information about the VCF Zarr format.
To create VCZ files from VCF and other formats, see the
bio2zarr project.
Vcztools provides a Python API to efficiently read VCZ data from local files and
remote object stores using
bcftools-compatible region and
variant filtering
syntax.
It aims to provide a drop-in replacement for a subset of bcftools functionality.
Currently supported are the view,
query and index -s/-n
commands; see bcftools emulation for worked examples.
We aim for 100% compatibility — if you notice a difference between the
output of vcztools and bcftools please
open an issue.
In addition to the bcftools-shaped commands, vcztools
provides format exporters for common downstream tools:
view-plink — PLINK 1 binary (
.bed/.bim/.fam); see the PLINK 1 file format page and the conversion walkthrough.view-bgen — Oxford BGEN (
.bgen/.sample/.bgen.bgi); see the BGEN file format page and the conversion walkthrough.
Development status#
vcztools is under active development and contributions are warmly welcomed
at the GitHub repository.