varona

Variant Annotation library and command line tool to read and annotate VCF file records, supplementing the information with data from the Ensembl VEP API. More information about the Varona is available in at the documentation site.

Installation

It's recommended to install varona into a Python virtual environment.

pip install --extra-index-url https://pypi.pohl.io/simple/ varona

Usage

varona input.vcf output.csv

Additionally, there are some options that can be used:

varona --help
## usage: varona [-h] [--log-level {debug,info,warning,error}] 
##   [--assembly {GRCH37,GRCH38}]
##   [--maf {FR,SAMPLES,BCFTOOLS}]
##   [--no-vep] [--vep-data VEP_DATA] [--version]
## 
## Annotate a VCF file.
## 
## options:
##   -h, --help            show this help message and exit
##   --log-level {debug,info,warning,error}
##                         Set the logging level (default: WARNING)
##   --assembly {GRCH37,GRCH38}
##                         genome assembly used in Ensembl VEP API (default: GRCh37)
##   --maf {FR,SAMPLES,BCFTOOLS}
##                         MAF calculation method (default: SAMPLES)
##   --no-vep              Skip VEP API querying (no effect if --vep-data is provided)
##   --vep-data VEP_DATA   Path to VEP output file
##   --version             Show program's version number and exit
##