.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH VCF2SCOARY "1" "January 2019" "vcf2scoary 1.6.16" "User Commands"
.SH NAME
vcf2scoary \- takes in vcf files and creates a presence/absence matrix of mutations in the Roary/Scoary format
.SH SYNOPSIS
vcf2scoary [\-h] [\-\-out OUT] [\-\-types TYPES] [\-\-version] [\-\-force]
<VCF_file>
.SH OPTIONS
.SS "positional arguments:"
.TP
<VCF_file>
The VCF file to convert to Roary/Scoary format
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-out\fR OUT
The path to the output file
.TP
\fB\-\-types\fR 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: \fB\-\-types\fR
snp,ins,del
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-\-force\fR
Force overwriting of output file. (If it already exists)
.PP
by Ola Brynildsrud (olbb@fhi.no)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.