Metadata-Version: 1.1
Name: zither
Version: 0.2
Summary: Command-line tool to pull raw depths and alt freqs from BAM file(s) based on an existing VCF, writing output as new VCF to stdout.
Home-page: https://github.com/umich-brcf-bioinf/Zither
Author: University of Michigan Bioinformatics Core
Author-email: bfx-zither@umich.edu
License: Apache
Description: ====== 
        Zither
        ======
        
        Command-line tool to pull raw depths and alt freqs from BAM file(s) based on an existing VCF, writing output as new VCF to stdout.
        
        .. image:: https://travis-ci.org/umich-brcf-bioinf/Zither.svg?branch=develop
            :target: https://travis-ci.org/umich-brcf-bioinf/Zither
            :alt: Build Status
        
        .. image:: https://coveralls.io/repos/umich-brcf-bioinf/zither/badge.svg?branch=develop&service=github
            :target: https://coveralls.io/github/umich-brcf-bioinf/zither?branch=develop
            :alt: Coverage Status
        
        
        
        The official repository is at:
        
        https://github.com/umich-brcf-bioinf/Zither
        
        ----------
        Quickstart
        ----------
        
        Read a single BAM file
        ======================
        
           $ zither --bam examples/explicit_bam/Sample_X.bam examples/explicit_bam/input.vcf > output.vcf 
        
        Given a VCF and a BAM file, read positions in the input VCF and corresponding pileups 
        from Sample_X.bam.
        
        
        Read a set of matched VCF sample names and BAM files
        ====================================================
        
           $ zither examples/matching_names/input.vcf > output.vcf 
        
        Given a VCF and a collection of BAM files whose file names 
        match the VCF sample names, reads positions from the 
        input VCF and corresponding BAM pileups.
        
        
        Explicitly map VCF sample names to BAM files
        ====================================================
        
           $ zither --mapping_file=examples/mapping_files/mapping_file.txt examples/mapping_files/input.vcf > output.vcf 
        
        Given a VCF, a collection of BAMs, and a file that maps sample names to BAM paths,
        reads positions from the input VCF and corresponding pileups 
        from BAM files names. 
        
        The mapping file is a tab-separated text file where each line has a sample 
        name and the path to the corresponding BAM file. Paths to BAM files can be 
        absolute or relative; relative paths are resolved relative to the directory 
        that contains the mapping file. 
        
        ====
        
        Email bfx-zither@umich.edu for support and questions.
        
        UM BRCF Bioinformatics Core 
        
        
        Changelog
        =========
        
        0.2 (9/3/2015)
        --------------
        - Adjusted tags to include total and unfiltered depth and alt freq.
        - Added basecall quality filtering
        - Added depth cutoff
        - Added support for Python3
        
        0.1 (8/6/2015)
        --------------
        Initial Release
        
        Zither is written and maintained by the University of Michigan 
        BRCF Bioinformatic Core; individual contributors include:
        
        - Chris Gates
        - Divya Kriti
Keywords: VCF bioinformatic exome-seq DNA-seq variant-call-format BAM
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
