Usage

Below is the usage information for the varona command:

usage: varona [-h] [--log-level {debug,info,warning,error}]
    [--assembly {GRCh37,GRCh38}]
    [--maf {FR,BCFTOOLS,SAMPLES}] input_vcf output_csv

Annotate a VCF file.

positional arguments:
  input_vcf             Path to the input VCF file
  output_csv            Path to the output CSV 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,BCFTOOLS,SAMPLES}
                        MAF calculation method (default: SAMPLES)

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.