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

LICENSE

Copyright 2011-2025 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2025 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.