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VCFGENO2HAPLO(1) vcfgeno2haplo (VCF transformation) VCFGENO2HAPLO(1)

vcfgeno2haplo

vcfgeno2haplo options []

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


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

0
Success
not 0
Failure

vcflib(1)

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

Erik Garrison and vcflib contributors.
vcfgeno2haplo (vcflib)
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