Hello everyone,

I'm new to genetics and seeking advice on SNP calling from both ddRAD data obtained online and my own WGS data. My goal is to identify SNPs that are consistent across both datasets for subsequent analysis. I'm considering two approaches:

Could someone explain the advantages of using stacks population for SNP calling in ddRAD data compared to the bcftools approach? Additionally, any insights or recommendations on the best approach for SNP calling in this scenario would be greatly appreciated.

Thank you all for your help in advance!