TY - JOUR T1 - Fast and efficient QTL mapper for thousands of molecular phenotypes JF - bioRxiv DO - 10.1101/022301 SP - 022301 AU - Halit Ongen AU - Alfonso Buil AU - Andrew Anand Brown AU - Emmanouil T. Dermitzakis AU - Olivier Delaneau Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/08/07/022301.abstract N2 - Motivation In order to discover quantitative trait loci (QTLs), multi-dimensional genomic data sets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing.Results We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted p-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot data sets can be now easily analyzed an order of magnitude faster than previous approaches.Availability Source code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/.Contact olivier.delaneau{at}unige.ch ER -