Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 20/01/12
  • Minor correction: 20/01/12

QTLMap : detection of QTL from experimental designs in outbred population

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System: UNIX-like, Windows
  • Current version: 0.8.3 - 14 october 2010
  • License(s): CeCILL
  • Status: beta release
  • Support: maintained, ongoing development
  • Designer(s): Pascale Le Roy, Jean-Michel Elsen, Helene Gilbert, Carole Moreno, Andres Legarra, Olivier Filangi
  • Contact designer(s): olivier.filangi@rennes.inra.fr
  • Laboratory, service: Animal Genetics


General software features


QTLMap is a software dedicated to the detection of QTL from experimental designs in outbred population. QTLMap software is developed by the Animal Genetics Division at INRA (French National Institute for Agronomical Research). The statistical techniques used are linkage analysis (LA) and linkage disequilibrium linkage analysis (LDLA) using interval mapping. Different versions of the LA are proposed from a quasi Maximum Likelihood approach to a fully linear (regression) model. The LDLA is a regression approach (Legarra and Fernando, 2009). The population may be sets of half-sib families or mixture of full- and half- sib families. The computations of Phase and Transmission probabilities are optimized to be rapid and as exact as possible. QTLMap is able to deal with large numbers of markers (SNP) and traits (eQTL).


  • QTL detection in half-sib families or mixture of full- and half-sib families
  • One or several linked QTL segregating in the population
  • Single trait or multiple trait
  • Nuisance parameters (e.g. sex, batch, weight...) and their interactions with QTL can be included in the analysis
  • Gaussian, discrete or survival (Cox model) data
  • Familial heterogeneity of variances (heteroscedasticity)
  • Can handle eQTL analyses
  • Computation of transmission and phase probabilities adapted to high throughput genotyping (SNP)
  • Empirical thresholds are estimated using simulations under the null hypothesis or permutations of trait values
  • Computation of power and accuracy of your design or any simulated design
Context in which the software is used

QTLMap source code is available under the CeCILL version 2.0 license, a GPL like license.


This software is used by genetic researchers to detect a region of the genome that controls an agronomic trait

Cluster Infrastructures

Software dependencies


  • Suite gcc (>=4.4)
  • CMake 2.6.4


Users mailing list : inscription

Publications related to the software

Legarra A, Fernando RL, 2009. Linear models for joint association and linkage QTL mapping. Genet Sel Evol., 41:43.

Elsen JM, Filangi O, Gilbert H, Le Roy P, Moreno C, 2009. A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps. Genet Sel Evol., 41:50.

Gilbert H., Le Roy P., Moreno C., Robelin D., Elsen J. M., 2008. QTLMAP, a software for QTL detection in outbred population. Annals of Human Genetics, 72(5): 694.

Gilbert H, Le Roy P., 2007. Methods for the detection of multiple linked QTL applied to a mixture of full and half sib families. Genet Sel Evol., 39(2):139-58.

Moreno C.R., Elsen J.M., Le Roy P., Ducrocq V., 2005. Interval mapping methods for detecting QTL affecting survival and time–to–event phenotypes. Genet. Res. Camb., 85 : 139-149.

Goffinet B, Le Roy P, Boichard D, Elsen JM, Mangin B, 1999. Alternative models for QTL detection in livestock. III. Heteroskedastic model and models corresponding to several distributions of the QTL effect.. Genet. Sel. Evol., 31, 341-350.

Mangin B, Goffinet B, Le Roy P, Boichard D, Elsen JM, 1999. Alternative models for QTL detection in livestock. II. Likelihood approximations and sire marker genotype estimations. Genet. Sel. Evol., 31, 225-237.

Elsen JM, Mangin B, Goffinet B, Boichard D, Le Roy P, 1999. Alternative models for QTL detection in livestock. I. General introduction. Genet. Sel. Evol., 31, 213-224