The basic workflow would be to map all your libraries against a single reference and look for SNPs with a analytical pipeline such as GATK's.

On the other hand, if you have GWAS data, then the markers have been called already (SNPs and INDELS).

After aligning your libraries against the reference genome, you can also use SAMTOOLS (as an alternative to GATK's) for SNP and INDELs detection, but before doing so make sure you remove the PCR duplicates. The resulted file with the variants (VCF file) should be filtered accordingly (i.e based on the coverage) and finally you should annotate the SNPs and INDELs for your GWAS (you can use Annovar or snpEff for the annotation).