---
name: "vcfgeno2haplo"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcfgeno2haplo"
---

# vcfgeno2haplo(1)

## NAME

**vcfgeno2haplo**

## SYNOPSIS

**vcfgeno2haplo** options \[\]

## DESCRIPTION

Convert genotype-based phased alleles within –window-size into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.

## OPTIONS

-

  ```
  options:
      -h, --help              Print this message
      -v, --version           Print version
      -r, --reference FILE    FASTA reference file
      -w, --window-size N     Merge variants at most this many bp apart (default 30)
      -o, --only-variants     Don't output the entire haplotype, just concatenate
                              REF/ALT strings (delimited by ":")
  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.