Convert gVCF into BED
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
```
========
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
```
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