positional arguments:¶

<VCF_file>

The VCF file to convert to Roary/Scoary format

optional arguments:¶

-h, --help

show this help message and exit

--out OUT

The path to the output file

--types TYPES

The types of variants to include in the output. NOTE: This works if TYPE=XX can be found in the INFO column of the vcf file. The special keyword ALL includes all types. This is the default setting. Common types are snp, mnp, ins, del and complex. Give as comma-separated list. Example: --types snp,ins,del

--version

show program's version number and exit

--force

Force overwriting of output file. (If it already exists)

by Ola Brynildsrud (olbb@fhi.no)