BiForce Toolbox has been developed as a collaboration between MRC Human Genetics Unit and the Finnish Microarray and Sequencing Centre. BiForce Toolbox addresses high throughput analysis of pair-wise epistasis in GWAS of quantitative and disease traits, and provides a solution for all commonly used computer systems. BiForce Toolbox is a stand-alone Java program that integrates bitwise computing with multithreaded parallelisation and thus allows rapid full pair-wise genome scans via a graphical user interface or the command line. Furthermore, it incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis. BiForce Toolbox is easy to use and has been applied in multiple studies of epistasis in large GWAS datasets, identifying interesting interaction signals and pathways.
We thank the financial support provided by BBSRC (Grant reference: BB/H024484/1) and MRC Core Fund.
IMPORTANT NOTICE. Note that BiForceToolbox may have inflated interaction test statistics in the situation when two SNPs are in strong linkage disequilibrium (LD) (usually closely located e.g. < 200 kb apart on a same chromosome) AND either or both of the SNPs have important marginal effects. That is to say the inflation is caused by marginal effects and LD jointly. Our survey of multiple traits suggests that the prevalence of the inflation issue is very low in general. Until the inflation problem will be fixed within the BiForceToolbox program we provide anInflationFix R-script for correcting the p-value of SNP-pairs found to be significant by the program. Usage of the script is given within the zip-file.
Contact: attila.gyenesei at csf.ac.at
- 2013Febr26: Until the inflation problem will be fixed within the BiForceToolbox program we provide an InflationFix R-script for correcting the p-value of SNP-pairs found to be significant by the program. Usage of the script is given within the zip-file.
- 2012Aug26: A new version of BiForceToolbox is available (version 2.01). A bug related to the calculation of the degree of freedom for quantitative traits has been fixed.
- 2012Aug25: A new version of GenABEL_to_BiForce.R script is available. The new script fixes a bug that was found in the old version.