debian man page for vcf-merge

VCF-MERGE(1)							   User Commands						      VCF-MERGE(1)

NAME
       vcf-merge - merge the bgzipped and tabix indexed VCF files

SYNOPSIS
       merge-vcf [OPTIONS] file1.vcf file2.vcf.gz ... > out.vcf

DESCRIPTION
       About: Merge the bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)

OPTIONS
       -c, --chromosomes <list|file>
	      Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future.

       -d, --remove-duplicates
	      If there should be two consecutive rows with the same chr:pos, print only the first one.

       -H, --vcf-header <file>
	      Use the VCF header

       -h, -?, --help
	      This help message.

       -r, --regions <list|file>
	      Do only the given regions (comma-separated list or one region per line in a file).

       -s, --silent
	      Try to be a bit more silent, no warnings about duplicate lines.

vcf-merge 0.1.5 						     July 2011							      VCF-MERGE(1)