NAME

       vcf2scoary  - takes in vcf files and creates a presence/absence matrix of mutations in the
       Roary/Scoary format

SYNOPSIS

       vcf2scoary [-h] [--out OUT] [--types TYPES] [--version] [--force] <VCF_file>

OPTIONS

   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)

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.