for testing rgfakePed.py --title '$title1' -o '$out_file1' -p '$out_file1.files_path' -c '$ncases' -n '$ntotal' -s '$nsnp' -w '$lowmaf' -v '$missingValue' -l '$outFormat' -d '$mafdist' -m '$missingRate' -M '$mendelRate' Uniform Triangular (more low frequency SNPs) Linkage format - separate .map file fbat style - marker names in a header row

.. class:: infomark This tool allows you to generate an arbitrary (sort of) synthetic genotype file (no attempt at LD - the markers are independent) with optional missingness, Mendel errors, minor allele frequency settings, family structure These might be used for testing under the null hypothesis of no association and are certainly useful for scale testing. Note that although it runs reasonably fast given it's a script, generating a large data set takes a while. An hour or so should get you a reasonable (3GB) sized simulated null data set.. A better simulator can easily be swapped in with this tool interface. ----- .. class:: warningmark This tool is very experimental **Attribution** Designed and written for the Rgenetics Galaxy tools copyright Ross Lazarus 2007 (ross.lazarus@gmail.com) Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html