===============================
VCF Toolz
===============================
.. Image showing the PyPI version badge - links to PyPI
.. image:: https://img.shields.io/pypi/v/vcftoolz.svg
:target: https://pypi.python.org/pypi/vcftoolz
.. Image showing the Travis Continuous Integration test status, commented out for now
.. .. image:: https://img.shields.io/travis/CFSAN-Biostatistics/vcftoolz.svg
.. :target: https://travis-ci.org/CFSAN-Biostatistics/vcftoolz
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.. image:: http://joss.theoj.org/papers/10.21105/joss.01144/status.svg
:target: https://doi.org/10.21105/joss.01144
Tools for working with Variant Call Format files.
VCF Toolz was developed by the United States Food
and Drug Administration, Center for Food Safety and Applied Nutrition.
* Free software
* Documentation: https://vcftoolz.readthedocs.io
* Source Code: https://github.com/CFSAN-Biostatistics/vcftoolz
* PyPI Distribution: https://pypi.python.org/pypi/vcftoolz
Features
--------
* Compares the snps in two or more VCF files.
* Lists the snps that are unique to each VCF file with full genotype information per snp.
* Lists the snps that are missing from each VCF file if present in at least two other VCF files.
* Generates Venn diagrams of positions and snps in the VCF files.
* Reports precision, recall, and F1 score when the truth is known.
* Reports the effectiveness of filtered variants when the truth is known.
* Reformat the VCF file in a tall-narrow format for easy viewing and diffs.
* Count samples, positions, calls, snps, indels, other variants, missing calls, and filter reasons.
* Plot calls along the length of the genome and show the location of filtered calls.
Citing VCF Toolz
--------------------------------------
To cite VCF Toolz, please reference the VCF Toolz paper:
https://doi.org/10.21105/joss.01144
License
-------
See the LICENSE file included in the VCF Toolz distribution.
History
=======
1.2.3 (2023-06-02)
------------------
* Fixed imports in our fork of pyvenn
1.2.2 (2023-06-01)
------------------
* Fixed broken Pyvenn dependency
1.2.1 (2023-05-09)
------------------
* Update PyVCF to PyVCF3
1.2.0 (2019-04-04)
---------------------
* Fix defect in narrow command wrongly printing ALT=. when GT=.
* Add the ``count`` command to count samples, positions, calls, snps, indels,
other variants, filtered calls, missing calls, and filter reasons.
* Add the ``plot`` command to plot calls along the length of the genome and show
the location of filtered calls.
* Change the text of the compare report to refer to "Calls", not "Sample snps".
* Drop support for Python 3.4, which is not supported by matplotlib.
* Add support for Python 3.7.
1.1.1 (2019-03-26)
---------------------
* Replace None with '.' when printing call data.
* Support VCF files with multiple alternate alleles per position.
1.1.0 (2019-02-06)
---------------------
* Support reading gzip compressed vcf files.
1.0.0 (2018-11-20)
---------------------
* First public release.
Raw data
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