Constructing linkage maps in the genomics era with MapDisto 2.0
Motivation: Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). Results: MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. Availability and Implementation: The program is available free of charge at mapdisto.free.fr.
| Main Authors: | , , |
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| Format: | Journal Article biblioteca |
| Language: | English |
| Published: |
Oxford University Press
2017-07-15
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| Subjects: | chromosome mapping, computer software, quantitative trait loci, genotyping, genetic markers, programas de ordenador, loci de rasgos cuantitativos, marcadores genéticos, |
| Online Access: | https://hdl.handle.net/10568/82887 https://doi.org/10.1093/bioinformatics/btx177 |
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