Metadata-Version: 2.1
Name: vcftoolz
Version: 1.2.1
Summary: Tools for working with Variant Call Format files.
Home-page: https://github.com/CFSAN-Biostatistics/vcftoolz
Author: Steve Davis
Author-email: steven.davis@fda.hhs.gov
License: BSD
Keywords: bioinformatics,NGS,vcftoolz
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: Freely Distributable
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
License-File: LICENSE
License-File: AUTHORS.rst
Requires-Dist: biopython
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: PyVCF3
Requires-Dist: matplotlib
Requires-Dist: matplotlib-venn

===============================
VCF Toolz
===============================


.. Image showing the PyPI version badge - links to PyPI
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        :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

.. Image showing the JOSS paper badge
.. 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
=======

1.2.0 (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.


