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Project 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

```

Release History

Release History

0.2

This version

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0.1.1

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0.1

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Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
gvcf2bed-0.2-py3.4.egg (5.8 kB) Copy SHA256 Checksum SHA256 3.4 Egg Sep 21, 2016
gvcf2bed-0.2-py3-none-any.whl (4.8 kB) Copy SHA256 Checksum SHA256 py3 Wheel Sep 21, 2016
gvcf2bed-0.2.tar.gz (4.0 kB) Copy SHA256 Checksum SHA256 Source Sep 21, 2016

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