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Qtltools specifications


Unique identifier OMICS_18457
Name Qtltools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.1
Stability Stable
Source code URL https://qtltools.github.io/qtltools/binaries/QTLtools_1.1_source.tar.gz
Maintained Yes




No version available


  • person_outline Olivier Delaneau
  • person_outline Emmanouil Dermitzakis

Publication for Qtltools

Qtltools citations


The effect of genetic variation on promoter usage and enhancer activity

Nat Commun
PMCID: 5677018
PMID: 29116076
DOI: 10.1038/s41467-017-01467-7

[…] Allelic consistency between genotype and CAGE tag sequences was assessed with the match BAM to VCF (MBV) methods (QTLtools package V1.1). Of the 156 samples passing the sequencing depth threshold, no amplification bias was detected and samples from two individuals, with suspicion of cross-sample contamination, we […]


A complete tool set for molecular QTL discovery and analysis

Nat Commun
PMCID: 5454369
PMID: 28516912
DOI: 10.1038/ncomms15452

[…] nning 1,000 permutations gives accurate adjusted P values while being ∼17 times faster than when implementing the standard permutation scheme with MatrixeQTL running on a BLAS-optimized R version. In QTLtools, we use exactly the same approach than in FastQTL: we approximate the permutation outcome with a beta distribution. We run this method on Geuvadis using 1,000 permutations and a cis-window of […]

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Qtltools institution(s)
Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland; Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
Qtltools funding source(s)
Supported by grants from European Commission SYSCOL FP7, European Research Council, Louis Jeantet Foundation, Swiss National Science Foundation, SystemsX, the NIH-NIMH (GTEx) and Helse Sør Øst.

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