FlexQTL protocols

FlexQTL computational protocol

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 pipelines

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 4.245 was used to identify […]

PMCID: 3338383
PMID: 22340438
DOI: 10.1186/1471-2229-12-25

[…] as presented in this paper. next, the inheritance of these cultivars over a pedigree was analysed using ibd estimates and the most likely linkage phases of alleles according to the software package flexqtl™ [17]. to graphically represent the flow of alleles over the pedigree, ibd estimates were loaded into pedimap [18]., the authors declare that they have no competing interests., tvd carried […]

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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