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

# vcfannotate(1)

## NAME

**vcfannotate**

## SYNOPSIS

**vcfannotate** options \[\]

## DESCRIPTION

Intersect the records in the VCF file with targets provided in a BED file. Intersections are done on the reference sequences in the VCF file. If no VCF filename is specified on the command line (last argument) the VCF read from stdin.

## OPTIONS

-

  ```
  options:
      -b, --bed   use annotations provided by this BED file
      -k, --key   use this INFO field key for the annotations
      -d, --default  use this INFO field key for records without annotations
  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.