---
name: "vcf-merge"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf-merge"
---

# vcf-merge(1)

merge the bgzipped and tabix indexed VCF files

## 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.