Quickstart

Before you run

1. harvest-tools VCF outputs indels in non standard format:
   • currently column based, not row based. excluding indel rows (default behavior) converts file into valid VCF format.
   • this will be updated in future version
2. Genbank annotation input:
   • Multiple Genbank files must be specified with multiple -g parameters
   • In addition, genome identifier (gi) must match the header of the reference fasta file

Download, install & run

harvest-tools is distributed as a precompiled binary. The three steps below represent the fastest way to start using the software:

On OSX:

1. wget https://github.com/marbl/harvest-tools/releases/download/v1.2/harvesttools-OSX64-v1.2.zip
2. tar -xvf harvesttools-OSX64-v1.2.tar.gz

On Linux:

1. wget https://github.com/marbl/harvest-tools/releases/download/v1.2/harvesttools-Linux64-v1.2.tar.gz
2. tar -xvf harvesttools-Linux64-v1.2.tar.gz

Basic usage:

From command-line:

harvesttools –x <input xmfa> -f <input reference fasta> -g <reference genbank formatted annotations> -n <newick formatted tree>

Advanced usage:

harvest-tools quick start for three example scenarios.

With reference & genbank file as input:

harvesttools -g <reference_genbank_file1> -r <reference fasta file> -x <XMFA file> -o hvt.ggr

With harvest-tools file as input, XMFA output:

harvesttools -i input.ggr -X output.xmfa

With harvest-tools file as input, fasta formatted SNP file as output:

harvesttools -i input.ggr -S output.snps

Command-line parameters:

• -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)

Primary output files

1. Compressed binary archive (GGR)

Additional output files

1. Variant Call Format (.vcf))

Example VCF output file:

 ##FILTER=<ID=IND,Description="Column contains indel">
 ##FILTER=<ID=N,Description="Column contains N">
 ##FILTER=<ID=LCB,Description="LCB smaller than 200bp">
 ##FILTER=<ID=CID,Description="SNP in aligned 100bp window with < 50% column % ID">
 ##FILTER=<ID=ALN,Description="SNP in aligned 100b window with > 20 indels">
 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  England1.fna.ref        Al-Hasa_18_2013.fna     Al-Hasa_1_2013.fna      England-Qatar_2012.fna  KSA-CAMEL-376.fna       NC_019843.2.fna
 gi|471258596|gb|KC164505.2|     1603    GTACTATGTA.CTTTGTGCCT   C       T       40      PASS    NA      GT      0       0       0       0       1       0
 gi|471258596|gb|KC164505.2|     1684    GGAACAAGGT.CACTCAAATT   C       T       40      PASS    NA      GT      0       0       0       0       1       0
 gi|471258596|gb|KC164505.2|     2502    ATATTCCCAT.CGGGAACCTA   C       T       40      PASS    NA      GT      0       0       0       0       1       0
 gi|471258596|gb|KC164505.2|     3275    TTCTCATGAG.ATTTCTGACG   A       G       40      PASS    NA      GT      0       1       1       0       1       0
 gi|471258596|gb|KC164505.2|     4396    TTCAAGCAGG.GAGTGTCGTG   G       T       40      PASS    NA      GT      0       1       1       0       0       0

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