Metadata-Version: 2.0
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
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: pyvcf (==0.6.8)

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

```

