.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH VCF-MERGE "1" "July 2011" "vcf-merge 0.1.5" "User Commands"
.SH NAME
vcf-merge \- merge the bgzipped and tabix indexed VCF files
.SH SYNOPSIS
.B merge-vcf
[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf.gz \fR... \fI> out.vcf\fR
.SH DESCRIPTION
About: Merge the bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz)
.SH OPTIONS
.TP
\fB\-c\fR, \fB\-\-chromosomes\fR <list|file>
Same as \fB\-r\fR, left for backward compatibility. Please do not use as it will be dropped in the future.
.TP
\fB\-d\fR, \fB\-\-remove\-duplicates\fR
If there should be two consecutive rows with the same chr:pos, print only the first one.
.TP
\fB\-H\fR, \fB\-\-vcf\-header\fR <file>
Use the VCF header
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.TP
\fB\-r\fR, \fB\-\-regions\fR <list|file>
Do only the given regions (comma\-separated list or one region per line in a file).
.TP
\fB\-s\fR, \fB\-\-silent\fR
Try to be a bit more silent, no warnings about duplicate lines.