snptranslate

NB!!

See the Wiki at https://github.com/haraldgrove/snptranslate/wiki for new info

The project snptranslate is for converting between the various genotype formats. The script will read one and one file from the input file and translate it as necessary before writing it to the output file.

Contact: [email protected]

HELP TEXT

Running the script with the -h option gives the following help text (the list of formats will automatically update when new formats are added):

usage: convSNP.py [-h] [-i GENOSFILE] [-n INFORM] [-p PEDIGREEFILE]
                  [-m MARKERFILE] [-o OUTPUTFILE] [-u OUTFORM] [-v VERBOSE]

snptranslate converts between the following SNP-formats: Plink, DMU, Geno, LD, Alphaimpute, Simplegeno

optional arguments:
  -h, --help            show this help message and exit
  -i GENOSFILE, --genotypes GENOSFILE
                        Input file
  -n INFORM, --informat INFORM
                        Input file format
  -p PEDIGREEFILE, --pedigree PEDIGREEFILE
                        Pedigree file
  -m MARKERFILE, --markers MARKERFILE
                        Marker file
  -o OUTPUTFILE, --output OUTPUTFILE
                        Output file
  -u OUTFORM, --outformat OUTFORM
                        Output file format
  -v VERBOSE, --verbose VERBOSE
                        Prints runtime info

EXAMPLE Translating a file called input.txt from DMU to Plink format and store it in a new file output.txt, with marker information located in a file 'marker.txt': convSNP.py -i input.txt -n DMU -o output.txt -u Plink -m marker.txt