Metadata-Version: 1.1
Name: vcftoolz
Version: 1.2.0
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
Description: ===============================
        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.
        
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
