Skip to content

Home

Jump to bottom
Sander W. van der Laan edited this page Aug 16, 2018 · 3 revisions

Introduction

GBASToolKit: a toolkit to perform gene-based association studies of your favourite GWAS using VEGAS21,2 or MAGMA3. It comprises various scripts in Perl, Python, R, and BASH.

All scripts are annotated for debugging purposes - and future reference. The only scripts the user should edit are:

  • the main job submission script gbastoolkit.qsub.sh,
  • gbastoolkit.conf, a configuration file with some system and analytical settings, and
  • gbastoolkit.list which contains a list of all the GWAS datasets.

Scripts will work within the context of a certain Linux environment (in this case a CentOS7 system on a SUN Grid Engine background); we have tested GBASToolKit on CentOS7, although with some edits it should work on OS X Sierra (version 10.11.[x]) too.

References

  1. https://doi.org/10.1016/j.ajhg.2010.06.009
  2. https://doi.org/10.1017/thg.2014.79
  3. https://doi.org/10.1371/journal.pcbi.1004219

The MIT License (MIT)

Copyright (c) 2015-2018 Sander W. van der Laan | s.w.vanderlaan [at] gmail [dot] com | swvanderlaan.github.io.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Reference: http://opensource.org.

Clone this wiki locally