Since the advent of Next Generation Sequencing, sequencing has been used for many applications, including obtaining genotypes for animal genomic selection. However, as full depth whole genome sequencing (WGS) is either unaffordable or inappropriate for certain applications, alternative approaches have been developed. Amongst them, double digested Restriction-site associated DNA sequencing (ddRAD-seq) offers a high sequencing depth on a targeted part of the genome. This type of approach reduces costs compared to full depth WGS and limits the inter-individual variability of a low depth WGS approach. A method such as ddRAD-seq could benefit the laying hen industry by providing low-cost genotyping, assuming it is of sufficient quality. The objective of this study was to evaluate the suitability of ddRAD-seq sequencing to detect variants and obtain bi-allelic SNP genotypes, using different sets of quality control filters. The study was conducted on a population of 50 males of a Rhode Island laying line for which sequences were obtained by ddRAD-seq with the Taq1/Pst1 enzyme couple and by 20X sequencing. First, the variant calling results were compared between 20X and ddRAD-seq. Then, the genotype concordance rate between ddRAD-seq and WGS 20X was calculated on the common SNPs. Finally, the variation of this concordance rate was calculated based on different filter combinations on the average sequencing depth (DP) per SNP and the SNP call rate (CR). 9,270,491 SNPs were genotyped in 20X and 350,490 in ddRAD-seq. The average SNP CR (55%) and the mean SNP DP value (11X) in ddRAD-seq were lower than in 20X (99% and 16X respectively). 327,364 SNPs were detected in both methods and were distributed on all the chromosomes. For these common SNPs, the mean of the concordance rate per SNP (CcR) between the genotypes obtained in ddRAD-seq and those obtained in 20X was on average 82%. The relationship between the CcR, the CR, the DP and the percentage of retained SNPs should allow future users of ddRAD-seq to choose the best filtering thresholds for their analyses.