Fulltext

Fast and efficient QTL mapper for thousands of molecular phenotypes

Ongen, Halit ; Buil, Alfonso ; Brown, Andrew Anand ; Dermitzakis, Emmanouil T. ; Delaneau, Olivier

In: Bioinformatics, 2016, vol. 32, no. 10, p. 1479-1485

Add to personal list
    Title
    • Fast and efficient QTL mapper for thousands of molecular phenotypes
    Author
    • Ongen, Halit. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    • Buil, Alfonso. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    • Brown, Andrew Anand. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    • Dermitzakis, Emmanouil T.. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    • Delaneau, Olivier. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
    Document Type
    • Postprint
    OAI-PMH Identifier
    • oai:doc.rero.ch:332946
    Summary
    Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets 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 datasets can be now easily analyzed an order of magnitude faster than previous approaches. Availability and implementation: Source code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/ Contact: emmanouil.dermitzakis@unige.ch or olivier.delaneau@unige.ch Supplementary information: Supplementary data are available at Bioinformatics online.