PT  - JOURNAL ARTICLE
AU  - Halit Ongen
AU  - Alfonso Buil
AU  - Andrew Anand Brown
AU  - Emmanouil T. Dermitzakis
AU  - Olivier Delaneau
TI  - Fast and efficient QTL mapper for thousands of molecular phenotypes
AID  - 10.1101/022301
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 022301
4099  - http://biorxiv.org/content/early/2015/08/07/022301.short
4100  - http://biorxiv.org/content/early/2015/08/07/022301.full
AB  - 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