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

# vcf-isec(1)

create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files

## NAME

vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files

## SYNOPSIS

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

## DESCRIPTION

About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.

-

  Note that lines from all files can be intermixed together on the output, which can yield unexpected results.

## OPTIONS

- **-C**, **--chromosomes** \<list\|file\>

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

- **-c**, **--complement**

  Output positions present in the first file but missing from the other files.

- **-d**, **--debug**

  Debugging information

- **-f**, **--force**

  Continue even if the script complains about differing columns.

- **-o**, **--one-file-only**

  Print only entries from the left-most file. Without **-o**, all unique positions will be printed.

- **-n**, **--nfiles** \[+-=\]\<int\>

  Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.

- **-p**, **--prefix** \<path\>

  If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)

- **-t**, **--tab** \<chr:pos:file\>

  Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)

- **-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.

## EXAMPLES

-

  bgzip file.vcf; tabix **-p** vcf file.vcf.gz bgzip file.tab; tabix **-s** 1 **-b** 2 **-e** 2 file.tab.gz