.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH HARVESTTOOLS "1" "March 2016" "harvesttools 1.2" "User Commands"
.SH NAME
harvesttools \- archiving and postprocessing for reference-compressed genomic multi-alignments
.SH SYNOPSIS
.B harvesttools
<options>
.SH DESCRIPTION
Harvesttools is a utility for creating and interfacing with Gingr files,
which are efficient archives that the Harvest Suite uses to store
reference-compressed multi-alignments, phylogenetic trees, filtered variants and
annotations. Though designed for use with Parsnp and Gingr, HarvestTools
can also be used for generic conversion between standard bioinformatics
file formats.
.SH OPTIONS
.HP
\fB\-i\fR <Gingr input>
.HP
\fB\-b\fR <bed filter intervals>,<filter name>,"<description>"
.HP
\fB\-B\fR <output backbone intervals>
.HP
\fB\-f\fR <reference fasta>
.HP
\fB\-F\fR <reference fasta out>
.HP
\fB\-g\fR <reference genbank>
.HP
\fB\-a\fR <MAF alignment input>
.HP
\fB\-m\fR <multi\-fasta alignment input>
.HP
\fB\-M\fR <multi\-fasta alignment output (concatenated LCBs)>
.HP
\fB\-n\fR <Newick tree input>
.HP
\fB\-N\fR <Newick tree output>
.HP
\fB\-\-midpoint\-reroot\fR (reroot the tree at its midpoint after loading)
.HP
\fB\-o\fR <Gingr output>
.HP
\fB\-S\fR <output for multi\-fasta SNPs>
.HP
\fB\-u\fR 0/1 (update the branch values to reflect genome length)
.HP
\fB\-v\fR <VCF input>
.HP
\fB\-V\fR <VCF output>
.HP
\fB\-x\fR <xmfa alignment file>
.HP
\fB\-X\fR <output xmfa alignment file>
.HP
\fB\-h\fR (show this help)
.HP
\fB\-q\fR (quiet mode)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.