---
name: "vcf2scoary"
section: "1"
platform: "linux"
package: "scoary"
version: "1.6.16-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf2scoary"
---

# vcf2scoary(1)

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

## 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.