Usage

Below is the usage information for the varona command:

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

The --maf option gives three options for calculating a minor allele frequency (MAF) value to include in the output CSV file. The BCFTOOLS option is available if Varona can find an installation of bcftools on the system.