To perform QTL mapping of the using GBS/RAD-seq one first need to perform a SNP calling using pipelines which could specifically developed for GBS/RAD-seq like TASSEL-GBS or WGS SNP calling pipelines like GATK that were adapted for GBS/RAD-seq, here you can find an example of such pipeline. Next you proceed with the SNP filtering and here a kind of art starts. I would recommend to filter for average genotype sequencing depth, proportion of genotyped individuals and MAF. Additionaly one should select SNPs that were genotyped in both parents, this step is crucial for genetic map construction. If you coverage is low it is possible to impute missing genotypes using tools like LB-impute pipeline specifically developed for mapping populations. Next one need to prepare a vcf filtered and imputed file for genetic map construction and QTL-mapping tools like r/qtl. Note for genetic map construction you need additionally filter your genotypes according to the expected segregation ratio i.e 1:2:1 for F2 cross and 1:1 for backcross (BC). Here is an example paper of QTL mapping based in GBS data. Good luck!