Metadata-Version: 1.1
Name: gvcf2bed
Version: 0.3.1
Summary: Convert gVCF into BED
Home-page: https://github.com/sndrtj/gvcf2bed
Author: Sander Bollen
Author-email: a.h.b.bollen@lumc.nl
License: MIT
Description: GVCF2BED
        ========
        
        This is a small tool to convert a gVCF file to BED. This is useful for
        extracting regions that pass a certain genotype quality threshold.
        
        Installation
        ------------
        
        gvcf2bed is now available through pypi with: ``pip install gvcf2bed``
        
        Requirements
        ------------
        
        -  Python 3.4+
        -  pyvcf
        -  cyvcf2
        
        For developers
        ~~~~~~~~~~~~~~
        
        -  pytest
        -  pytest-cov
        
        Changelog
        ---------
        
        0.3.1
        ~~~~~
        
        -  Fix a bug for variants where GQ is not defined.
        
        0.3
        ~~~
        
        -  Use ``cyvcf2`` by default in tool. This results in a speed-up of
           approximately 8-10x. Existing API has not changed, and will still
           work with ``pyvcf``.
        -  Add separate filter for non-variants, as GQ scores may have a
           different distribution on non-variant records than on variant
           records.
        
        Usage
        -----
        
        ::
        
            usage: gvcf2bed [-h] -I INPUT -O OUTPUT [-s SAMPLE] [-q QUALITY]
                            [-nq NON_VARIANT_QUALITY] [-b]
        
            Create a BED file from a gVCF. Regions are based on a minimum genotype
            quality. The gVCF file must contain a GQ field in its FORMAT fields. GQ scores
            of non-variants records have a different distribution from the GQ score
            distribution of variant records. Hence, an option is provided to set a
            different threshold for non-variant positions.
        
            optional arguments:
              -h, --help            show this help message and exit
              -I INPUT, --input INPUT
                                    Input gVCF
              -O OUTPUT, --output OUTPUT
                                    Output bed file
              -s SAMPLE, --sample SAMPLE
                                    Sample name in VCF file to use. Will default to first
                                    sample (alphabetically) if not supplied
              -q QUALITY, --quality QUALITY
                                    Minimum genotype quality (default 20)
              -nq NON_VARIANT_QUALITY, --non-variant-quality NON_VARIANT_QUALITY
                                    Minimum genotype quality for non-variant records
                                    (default 20)
              -b, --bedgraph        Output in bedgraph mode
        
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
