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. FastQTL also provides a modular base onto which new functionalities are being implemented, such as fine mapping of causal variants, conditional analysis to discover multiple independent QTLs per phenotype and interaction analysis to discover sex or disease specific QTLs.

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FastQTL classification

FastQTL specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
C++
Version:
FastQTL version 2-184
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable

Publications

  • (Ongen et al., 2015) Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics.
    PMID: 26708335

Credits

Institution(s)

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

Funding source(s)

This research is supported by grants from European Commission SYSCOL FP7, European Research Council, Louis Jeantet Foundation, Swiss National Science Foundation, SystemsX, the NIHNIMH (GTEx) and Helse Sør Øst.

Link to literature

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