---
name: "vcfintersect"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcfintersect"
---

# vcfintersect(1)

## NAME

**vcfintersect**

## SYNOPSIS

**vcfintersect** options \[\]

## DESCRIPTION

VCF set analysis

## OPTIONS

-

  ```
  options:
      -b, --bed FILE            use intervals provided by this BED file
      -R, --region REGION       use 1-based tabix-style region (e.g. chrZ:10-20), multiples allowed
      -S, --start-only          don't use the reference length information in the record to determine
                                overlap status, just use the start posiion
      -v, --invert              invert the selection, printing only records which would
                                  not have been printed out
      -i, --intersect-vcf FILE  use this VCF for set intersection generation
      -u, --union-vcf FILE      use this VCF for set union generation
      -w, --window-size N       compare records up to this many bp away (default 30)
      -r, --reference FILE      FASTA reference file, required with -i and -u
      -l, --loci                output whole loci when one alternate allele matches
      -m, --ref-match           intersect on the basis of record REF string
      -t, --tag TAG             attach TAG to each record's info field if it would intersect
      -V, --tag-value VAL       use this value to indicate that the allele is passing
                                '.' will be used otherwise.  default: 'PASS'
      -M, --merge-from FROM-TAG
      -T, --merge-to   TO-TAG   merge from FROM-TAG used in the -i file, setting TO-TAG
                                in the current file.
  For bed-vcf intersection, alleles which fall into the targets are retained.
  Haplotype aware intersection, union and complement. Use for intersection and union of VCF files: unify on equivalent alleles within window-size bp
  as determined by haplotype comparison alleles.
  type: transformation
  ```

## EXIT VALUES

- **0**

  Success

- **not 0**

  Failure

## SEE ALSO

[**vcflib**(1)](/vcflib/1.md)

## OTHER

## LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

## AUTHORS

Erik Garrison and vcflib contributors.