from linkage format to SNPTEST Marchini files
rgGTOOL.py $i $o $discrete $logf $outdir
**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
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**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.