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.