Scroll to navigation

VCF2SCOARY(1) User Commands VCF2SCOARY(1)


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>


positional arguments:

The VCF file to convert to Roary/Scoary format

optional arguments:

show this help message and exit
The path to the output file
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
show program's version number and exit
Force overwriting of output file. (If it already exists)

by Ola Brynildsrud (


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

January 2019 vcf2scoary 1.6.16