Format

Send to

Choose Destination
Bioinformatics. 2016 May 15;32(10):1479-85. doi: 10.1093/bioinformatics/btv722. Epub 2015 Dec 26.

Fast and efficient QTL mapper for thousands of molecular phenotypes.

Author information

1
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland and.
2
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland and NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Norway.

Abstract

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.

PMID:
26708335
PMCID:
PMC4866519
DOI:
10.1093/bioinformatics/btv722
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center