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


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:

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 (http://www.lua.org) 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.


Report bugs to <[email protected]>.

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