GT-SNPPER(1)

💖 GT-SNPPER(1) 💖

okay bestie, welcome to the GenomeTools Manual page for gt-snpper — yes it's a manpage, no it does not have to be boring, let's go ✨

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🌸 NAME 🌸

gt-snpper — annotates SNPs based on how they affect the genome, as described by a genomic annotation. it's giving "what did this tiny letter swap actually do" energy 💅

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✨ SYNOPSIS ✨

gt snpper [option ...] GFF3_file [GVF_file]

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🦋 DESCRIPTION 🦋

🎀 OPTIONS 🎀

• -trans_table [value] — the NCBI translation table number, and you literally get to pick from this whole menu:
  • 1: Standard
  • 2: Vertebrate Mitochondrial
  • 3: Yeast Mitochondrial
  • 4: Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
  • 5: Invertebrate Mitochondrial
  • 6: Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
  • 9: Echinoderm Mitochondrial; Flatworm Mitochondrial
  • 10: Euplotid Nuclear
  • 11: Bacterial, Archaeal and Plant Plastid
  • 12: Alternative Yeast Nuclear
  • 13: Ascidian Mitochondrial
  • 14: Alternative Flatworm Mitochondrial
  • 15: Blepharisma Macronuclear
  • 16: Chlorophycean Mitochondrial
  • 21: Trematode Mitochondrial
  • 22: Scenedesmus obliquus Mitochondrial
  • 23: Thraustochytrium Mitochondrial
  • 24: Pterobranchia Mitochondrial
  • 25: Candidate Division SR1 and Gracilibacteria (default: 1)
• -seqfile [filename] — tells it which sequence file to pull the sequences from (default: undefined) 🧬
• -encseq [filename] — sets the encoded sequence indexname to pull the sequences from (default: undefined)
• -seqfiles — sets the sequence files to extract the features from; use -- to terminate the list of sequence files 📋
• -matchdesc [yes|no] — searches the sequence descriptions in the input files for the sequence IDs you want (in GFF3), and reports the first match (default: no)
• -matchdescstart [yes|no] — matches the sequence descriptions from the input files against the desired sequence IDs (in GFF3) exactly, from the beginning all the way to the first whitespace (default: no)
• -usedesc [yes|no] — uses sequence descriptions to map the sequence IDs (in GFF3) onto actual sequence entries. if a description has a sequence range in it (like III:1000001..2000000), then the first part becomes the sequence ID (III) and the first range position becomes the offset (1000001) (default: no)
• -regionmapping [string] — sets the file that contains the sequence-region-to-sequence-file mapping (default: undefined) 🗺️
• -o [filename] — redirects output into the file you specify (default: undefined)
• -gzip [yes|no] — writes a gzip-compressed output file (default: no)
• -bzip2 [yes|no] — writes a bzip2-compressed output file (default: no)
• -force [yes|no] — forces writing to the output file (default: no)
• -help — shows help and dips ✌️
• -version — shows version info and dips ✌️

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🌈 File format for option -regionmapping 🌈

the file you hand to option -regionmapping defines a “mapping”. a mapping takes the sequence-region entries in the GFF3_file and maps them to a sequence file that holds the matching sequence. you can define mappings in one of these two forms, pick your fighter:

mapping = {
  chr1  = "hs_ref_chr1.fa.gz",
  chr2  = "hs_ref_chr2.fa.gz"
}

or

function mapping(sequence_region)
  return "hs_ref_"..sequence_region..".fa.gz"
end

the first form defines a Lua (<http://www.lua.org>) table named “mapping” that maps each sequence region to its corresponding sequence file. the second one defines a Lua function called “mapping”, and that function has to return the sequence file name when you call it with the sequence_region as its argument. iykyk 💫

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😭 REPORTING BUGS 😭

found a bug? spill it here: <https://github.com/genometools/genometools/issues>.

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ngl this page is from GenomeTools 1.6.6, dated 11/09/2025. that's the whole footer bestie, we did it, slay 💅✨🦋