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% VCFGENO2HAPLO(1) vcfgeno2haplo (vcflib) | vcfgeno2haplo (VCF transformation)
% Erik Garrison and vcflib contributors
# NAME
**vcfgeno2haplo**
# SYNOPSIS
**vcfgeno2haplo** [options] [<vcf file>]
# 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](./vcflib.md)(1)
# OTHER
## Source code
[vcfgeno2haplo.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcfgeno2haplo.cpp)
# LICENSE
Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.
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