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

# vcf-compare(1)

compare bgzipped and tabix indexed VCF files

## NAME

vcf-compare - compare bgzipped and tabix indexed VCF files

## SYNOPSIS

**compare-vcf** \[*OPTIONS*\] *file1.vcf file2.vcf* ...

## DESCRIPTION

About: Compare 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**, **--debug**

  Debugging information. Giving the option multiple times increases verbosity

- **-H**, **--cmp-haplotypes**

  Compare haplotypes, not only positions

- **-m**, **--name-mapping** \<list\|file\>

  Use with **-H** when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping per line in a file. The names are colon separated and must appear in the same order as the files on the command line.

- **-R**, **--refseq** \<file\>

  Compare the actual sequence, not just positions. Use with **-w** to compare indels.

- **-r**, **--regions** \<list\|file\>

  Process the given regions (comma-separated list or one region per line in a file).

- **-s**, **--samples** \<list\>

  Process only the listed samples. Excluding unwanted samples may increase performance considerably.

- **-w**, **--win** \<int\>

  In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a SNP or an indel).

- **-h**, -?, **--help**

  This help message.