FlexQTL statistics

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FlexQTL specifications


Unique identifier OMICS_18988
Name FlexQTL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.99
Stability Stable
Maintained Yes



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  • person_outline Maria José Aranzana <>

Publication for FlexQTL

FlexQTL in pipeline

PMCID: 5676184
PMID: 29138689
DOI: 10.1038/hortres.2017.62

[…] for allele visualization and scoring., snp markers covering the qtl confidence interval region were chosen for haplotyping. phased haplotype information was obtained for each individual from the flexqtl output and the number of individuals represented by haplotypes and diplotypes by each of the 15 snp markers was calculated using excel. haploview version 4.2 was used to identify […]

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FlexQTL in publications

PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] we also anticipate that more powerful qtl analyses can be performed by combining information over multiple populations. approaches such as pedigree-informed analyses, implemented for diploids in the flexqtl software (), could overcome some of the limitations imposed by the restrictions on population types in software for polyploids. however, it may take some time before such tools become […]

PMCID: 5878828
PMID: 29619228
DOI: 10.1038/s41438-018-0021-6

[…] gaps may be caused by the lack of markers covering heterochromatic pericentromeric regions. this consensus map will serve as one of the basic components required in a pedigree-based qtl analysis (flexqtl™) to facilitate marker–trait association studies., synteny among several rosaceae crops has been reported in many studies, including prunus crops themselves (almond, peach, apricot, […]

PMCID: 5830435
PMID: 29507735
DOI: 10.1038/s41438-018-0016-3

[…] the format of its input files are compatible with output files from genomestudio (illumina inc., san diego, ca, usa; http://www.illumina.com)., fruitbreedomics successfully extended the software flexqtl for use on snp markers. flexqtl was developed in the previous eu-hidras project to enable multi-family analyses and was ready for the use of ssr markers. as thousands snp markers […]

PMCID: 5676184
PMID: 29138689
DOI: 10.1038/hortres.2017.62

[…] and in conjunction with the axiom istraw90 snp array has become a powerful tool for high-resolution qtl mapping., using this pedigree-based qtl analysis (pba) approach, implemented through flexqtl, provides advantages over traditional bi-parental population methods, allowing for a qtl to be evaluated in numerous genetic backgrounds while simultaneously increasing the chances […]

PMCID: 5461300
PMID: 28638387
DOI: 10.3389/fpls.2017.00858

[…] and the similar small size of both genetic maps. then sets of single snps were integrated into haploblocks, corresponding to successive 1 cm segments. haplotypes were composed using the software flexqtl™ (www.flexqtl.nl) and pedihaplotyper (voorrips et al., )., indices used in qtl analysis were bbi_res_norm_ax, γax, bbi_res_norm_pred, γpred, ent¯g, ent¯glmm,g, the blups for genotypes × […]

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FlexQTL institution(s)
IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain; Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, TN, Italy; Hendrix Genetics Research, Technology & Services B.V., Boxmeer, Netherlands; Plant Breeding, Wageningen University and Research Droevendaalsesteeg 1, Wageningen, Netherlands; IRTA, FruitCentreParc Cientific i Tecnològic Agroalimentari de Lleida (PCiTAL), Lleida, Spain; PTP Science Park, Lodi, Italy; Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy; Consiglio per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, Roma, Italy; BFP, INRA, Villenave d’Ornon, France; GAFL, INRA, Montfavet, France; Università degli Studi di Milano, DiSAA, Milan, Italy; IRHS, INRA, SFR 4207 QuaSaV, Beaucouze, France
FlexQTL funding source(s)
Supported by the EU seventh Framework Programme by the FruitBreedomics project Nu. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops; IRTA-CRAG group received financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV-2015-0533)” and through the project AGL2015-68329-R, and from the CERCA Programme/Generalitat de Catalunya.

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