NAME

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

SYNOPSIS

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

DESCRIPTION

       -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)

       -seqfiles
           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)

       -help
           display help and exit

       -version
           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"
           }

       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” 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.

REPORTING BUGS

       Report bugs to <gt-users@genometools.org>.