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

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

vcf2scoary 1.6.16                                 January 2019                                     VCF2SCOARY(1)

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

positionalarguments:
       <VCF_file>
              The VCF file to convert to Roary/Scoary format

   optionalarguments:-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)

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