vcfgeno2haplo

Authors

       Erik Garrison and vcflib contributors.

vcfgeno2haplo (vcflib)                                                                          VCFGENO2HAPLO(1)

Description

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

Exit Values

0      Success

       not0  Failure

License

       Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.  MIT licensed.   Copyright  2020-2024  (C)
       Pjotr Prins.

Name

vcfgeno2haplo

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