from linkage format to SNPTEST Marchini files rgGTOOL.py $i $o $discrete $logf $outdir Discrete Continuous **Syntax** - **Genotype file** is the input linkage format pedigree and corresponding map file - **Discrete** is the type of phenotype in the affection column - **Output name** is the file name (.gen and .sample will be added) for the new SNPTEST compatible file **Note on Discrete** See GTOOL_ documentation link below for more details. Briefly, if your linkage format pedigree file has 1/2 in column 6 for control/case respectively, setting this to Yes will create two complete sets of output files distinguished by 1 and 2 respectively. otherwise, affection status is assumed to contain a continuous phenotype and a single output set is produced **Summary** Code used here from Jonathon Marchini's group - see documentation at GTOOL_. .. _GTOOL: http://www.stats.ox.ac.uk/~marchini/software/gwas/gtool.html ----- **Attribution** Originally designed and written for the Rgenetics series of Galaxy tools by ross lazarus (ross.lazarus@gmail.com), who didn't write GTOOL_ but wishes he had.