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Bioinformatics. 2014 Jul 1;30(13):1940-1. doi: 10.1093/bioinformatics/btu149. Epub 2014 Mar 14.

FSuite: exploiting inbreeding in dense SNP chip and exome data.

Author information

1
Inserm, U946, Genetic variability and human diseases, Paris, 75010, Université Paris Sud, Kremlin-Bicêtre, 94270, Fondation Jean Dausset CEPH, Paris, 75010, Université Paris-Diderot, UMR 946, Institut Universitaire d'Hématologie, Paris, 75475, Inserm, U1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest, 29218 and Centre Hospitalier Régional Universitaire de Brest, Brest, 29200, France Inserm, U946, Genetic variability and human diseases, Paris, 75010, Université Paris Sud, Kremlin-Bicêtre, 94270, Fondation Jean Dausset CEPH, Paris, 75010, Université Paris-Diderot, UMR 946, Institut Universitaire d'Hématologie, Paris, 75475, Inserm, U1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest, 29218 and Centre Hospitalier Régional Universitaire de Brest, Brest, 29200, France.
2
Inserm, U946, Genetic variability and human diseases, Paris, 75010, Université Paris Sud, Kremlin-Bicêtre, 94270, Fondation Jean Dausset CEPH, Paris, 75010, Université Paris-Diderot, UMR 946, Institut Universitaire d'Hématologie, Paris, 75475, Inserm, U1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest, 29218 and Centre Hospitalier Régional Universitaire de Brest, Brest, 29200, France.

Abstract

FSuite is a user-friendly pipeline developed for exploiting inbreeding information derived from human genomic data. It can make use of single nucleotide polymorphism chip or exome data. Compared with other software, the advantage of FSuite is that it provides a complete suite of scripts to describe and use the inbreeding information. It includes a module to detect inbred individuals and estimate their inbreeding coefficient, a module to describe the proportion of different mating types in the population and the individual probability to be offspring of different mating types that can be useful for population genetic studies. It also allows the identification of shared regions of homozygosity between affected individuals (homozygosity mapping) that can be used to identify rare recessive mutations involved in monogenic or multifactorial diseases.

AVAILABILITY AND IMPLEMENTATION:

FSuite is developed in Perl and uses R functions to generate graphical outputs. This pipeline is freely available under GNU GPL license at: http://genestat.cephb.fr/software/index.php/FSuite.

PMID:
24632498
DOI:
10.1093/bioinformatics/btu149
[Indexed for MEDLINE]
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