vcf_filter
helper scripts for Variant Call Format (VCF) parser
Install
- All systems
-
curl cmd.cat/vcf_filter.sh
- Debian
-
apt-get install pyvcf - Ubuntu
-
apt-get install pyvcf - Kali Linux
-
apt-get install pyvcf - Windows (WSL2)
-
sudo apt-get updatesudo apt-get install pyvcf - Raspbian
-
apt-get install pyvcf - Dockerfile
- dockerfile.run/vcf_filter
pyvcf
helper scripts for Variant Call Format (VCF) parser
The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project. The intent of this module is to mimic the ``csv`` module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. ``vcf`` will attempt to parse the content of each record based on the data types specified in the meta-information lines -- specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings. This package provides helper scripts using python3-pyvcf.