vcf2scoary - takes in vcf files and creates a presence/absence
matrix of mutations in the Roary/Scoary format
vcf2scoary [-h] [--out OUT] [--types TYPES] [--version] [--force]
<VCF_file>
- <VCF_file>
- The VCF file to convert to Roary/Scoary format
- -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)
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.