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