VCFGENO2HAPLO

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 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS

Erik Garrison and vcflib contributors.