% VCFGENO2HAPLO(1) vcfgeno2haplo (vcflib) | vcfgeno2haplo (VCF transformation) % Erik Garrison and vcflib contributors

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)

OTHER

Source code

vcfgeno2haplo.cpp

LICENSE

Copyright 2011-2026 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2026 (C) Pjotr Prins.