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>