Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population

This dataset, intended for QTL detection and genomic prediction, includes : 1) the SNP genotyping data, in vcf format, obtained by GBS in a grapevine bi-parental population, and the script for formatting the data before building the genetic map; 2) the script and custom R functions used for building the map; 3) the script for checking map quality; 4) the consensus genetic map generated from these data, both in R/qtl format and recoded into additive gene-dose. The population is a pseudo-F1 progeny of 188 offsprings of Vitis vinifera L. from a reciprocal cross between cultivars Syrah and Grenache, made at Vassal (French National Grapevine Germplasm Collection, Domaine de Vassal, 34340 Marseillan-Plage, France) in 1995. More details about this Syrah x Grenache (SxG) progeny can be found in Adam-Blondon et al. (2004) and Fournier-Level et al. (2009). SNP genotyping data are in the form of the vcf file obtained after SNP calling and filtering (see details below). All scripts are given as Rmd files including R and bash commands. Genetic maps were built with Carthagene and Lep-MAP3, and checked with custom R scripts and R/qtl.