Goats were domesticated 10,500 years ago with the aim of supplying milk, meat and fibres. Since then, breeds have specialized and adapted to their local environment developing specific genetic profiles. The VarGoats project is an international resequencing program, which aims at covering at best the genetic diversity of the Capra species. To date the sequence data 829 Capra hircus of various breeds and geographical origins. Variant calling led to the identification of a total of 110,193,942 variants on the 29 autosomal chromosomes. Quality checks were applied to sequence variants using various indicators: quality, depth, minor allele frequency and position. For French Alpine and Saanen breeds the concordance with 50k genotypes (CaprineSNP50 BeadChip) was checked. Mean concordance rate was 98.22% and ranged from 94.00 to 99.96% among individuals. Imputation was tested on the 23,338,436 filtered variants using FImpute software. Pedigree was provided and imputation was performed in a within-breed leaveone-out scenario. Imputation quality was checked for 4 individuals on all chromosomes and for every sequenced animal on chromosome 29. Mean concordance rate for chromosome 29 ranged from 73.49 to 85.71% and from 72.72 to 79.27% in Alpine and Saanen breeds respectively. On all chromosomes, average correlation between true and imputed sequence were 0.77 and 0.76 in Alpine and Saanen respectively. Imputation was then applied to a population of 1,129 French Alpine and Saanen males with at least 10 daughters phenotypes. Association analysis was performed on production and functional traits using polygenic models with the GCTA software. Using genotype data imputed to sequence level allowed to improve the significance of QTL previously identified with 50k SNP-chip only. In Saanen breed, 1.6 Mb region on chromosome 19 was identified as significantly linked to 4 conformation traits, 3 semen production traits, somatic cell count, milk yield and protein and fat contents. These researches provided insights on how to implement a quality check, imputation that will ensure the quality of subsequent analyses, and on new SNPs to be added to the 50k SNP-chip.