harvesttools(1)
archiving and postprocessing for reference-compressed genomic multi-alignments
Description
HARVESTTOOLS
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
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-i <Gingr input> |
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-b <bed filter intervals>,<filter name>,"<description>" |
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-B <output backbone intervals> |
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-f <reference fasta> |
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-F <reference fasta out> |
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-g <reference genbank> |
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-a <MAF alignment input> |
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-m <multi-fasta alignment input> |
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-M <multi-fasta alignment output (concatenated LCBs)> |
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-n <Newick tree input> |
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-N <Newick tree output> |
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--midpoint-reroot (reroot the tree at its midpoint after loading) |
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-o <Gingr output> |
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-S <output for multi-fasta SNPs> |
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-u 0/1 (update the branch values to reflect genome length) |
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-v <VCF input> |
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-V <VCF output> |
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-x <xmfa alignment file> |
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-X <output xmfa alignment file> |
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-h (show this help) |
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-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.