---
name: "harvesttools"
section: "1"
platform: "linux"
package: "harvest-tools"
version: "1.3-8+b5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/harvesttools"
---

# harvesttools(1)

archiving and postprocessing for reference-compressed genomic multi-alignments

## NAME

harvesttools - archiving and postprocessing for reference-compressed genomic multi-alignments

## SYNOPSIS

**harvesttools** \<options\>

## 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.

## OPTIONS

**-i** \<Gingr input\>

**-b** \<bed filter intervals\>,\<filter name\>,"\<description\>"

**-B** \<output backbone intervals\>

**-f** \<reference fasta\>

**-F** \<reference fasta out\>

**-g** \<reference genbank\>

**-a** \<MAF alignment input\>

**-m** \<multi-fasta alignment input\>

**-M** \<multi-fasta alignment output (concatenated LCBs)\>

**-n** \<Newick tree input\>

**-N** \<Newick tree output\>

**--midpoint-reroot** (reroot the tree at its midpoint after loading)

**-o** \<Gingr output\>

**-S** \<output for multi-fasta SNPs\>

**-u** 0/1 (update the branch values to reflect genome length)

**-v** \<VCF input\>

**-V** \<VCF output\>

**-x** \<xmfa alignment file\>

**-X** \<output xmfa alignment file\>

**-h** (show this help)

**-q** (quiet mode)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.