Important information

Versions up to and including 1.2, suffer from a bug in reading missing genotypes in VCF/BCF files. This bug affects variants with a DS field in their genotype's FORMAT and have a missing genotype (DS field is .) in one of the samples, in which case genotypes for all the samples are set to missing, effectively removing this variant from the analyses. Affected modes: cis, correct, gwas, pca, rep, trans, rtc-union

Please use the man pages for documentation. The previous documentation is still available but is now OUTDATED, and will be removed in the future.

General information

QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps. For the moment, QTLtools can perform the following tasks:

QTLtools has been implemented in C++ and has some nice properties:

QTLtools is mostly developed by :

For questions and/or bug reports concerning QTLtools, please contact:

When QTLtools is used, please cite one of the following papers:

Thursday 27th August 2020<