Metadata-Version: 1.1
Name: gvcf2bed
Version: 0.2
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
        
        ### For developers
        
        * pytest
        * pytest-cov
        
        
        ## Usage
        
        ```
        usage: gvcf2bed [-h] -I INPUT -O OUTPUT [-s SAMPLE] [-q 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.
        
        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)
          -b, --bedgraph        Output in bedgraph mode
        
        ```
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
