NAME¶

pxvcf2fa - convert vcf file to fasta

SYNOPSIS¶

pxvcf2fa [OPTIONS]...

DESCRIPTION¶

Convert vcf file to fasta. Currently only handles haploid data; phased data will come soon. Data can be read from a file or STDIN.

OPTIONS¶

-s, --seqf=FILE

input vcf file, STDIN otherwise

-u, --uppercase

export characters in uppercase

-o, --outf=FILE

output fasta sequence file, STOUT otherwise

-h, --help

display this help and exit

-V, --version

display version and exit

-C, --citation

display phyx citation and exit

CITATION¶

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

AUTHOR¶

Written by Joseph W. Brown

REPORTING BUGS¶

Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>

COPYRIGHT¶

Copyright © 2013-2021 FePhyFoFum License GPLv3