Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (
Help us improve Python packaging - Donate today!

Convert gVCF into BED

Project Description

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.


gvcf2bed is now available through pypi with: pip install gvcf2bed


  • Python 3.4+
  • pyvcf
  • cyvcf2

For developers

  • pytest
  • pytest-cov



  • 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: 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

Release History

This version
History Node


History Node


History Node


History Node


Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, Size & Hash SHA256 Hash Help File Type Python Version Upload Date
(5.9 kB) Copy SHA256 Hash SHA256
Wheel py3 Jun 8, 2017
(5.0 kB) Copy SHA256 Hash SHA256
Source None Jun 8, 2017

Supported By

Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Google Google Cloud Servers