Provided by: harvest-tools_1.3-4build1_amd64
harvesttools - archiving and postprocessing for reference-compressed genomic multi- alignments
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.
-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)
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.