gt-snpper - Annotates SNPs according to their effect on the genome as given by a genomic annotation.


gt snpper [option …] GFF3_file [GVF_file]


-trans_table [value]

NCBI translation table number, choose from:

  • 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]

set the sequence file from which to take the sequences (default: undefined)

-encseq [filename]

set the encoded sequence indexname from which to take the sequences (default: undefined)


set the sequence files from which to extract the features use -- to terminate the list of sequence files

-matchdesc [yes|no]

search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)

-matchdescstart [yes|no]

exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)

-usedesc [yes|no]

use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (III) and the first range position as offset (1000001) (default: no)

-regionmapping [string]

set file containing sequence-region to sequence file mapping (default: undefined)

-o [filename]

redirect output to specified file (default: undefined)

-gzip [yes|no]

write gzip compressed output file (default: no)

-bzip2 [yes|no]

write bzip2 compressed output file (default: no)

-force [yes|no]

force writing to output file (default: no)


display help and exit


display version information and exit

File format for option -regionmapping:

The file supplied to option -regionmapping defines a “mapping”. A mapping maps the sequence-region entries given in the GFF3_file to a sequence file containing the corresponding sequence. Mappings can be defined in one of the following two forms:

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


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

The first form defines a Lua ( table named “mapping” which maps each sequence region to the corresponding sequence file. The second one defines a Lua function “mapping”, which has to return the sequence file name when it is called with the sequence_region as argument.