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gt-snpper - Online in the Cloud

Run gt-snpper in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gt-snpper that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 <[email protected]>.

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