Fast and efficient QTL mapper for thousands of molecular phenotypes

Fast and efficient QTL mapper for thousands of molecular phenotypes

Halit Ongen, Alfonso Buil, Andrew Brown, Emmanouil Dermitzakis, Olivier Delaneau

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


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