Genotyping by Sequencing in Grape - Stacks or Tassel?

Genotyping by sequencing (GBS) is a powerful method for assaying populations of individuals for hundreds of thousands of genetic markers.  The optimal strategy employed for data collection and analysis depends on the kind of biological question being asked and the genomic resources already available.  We have collected data from a bi-parental population in grape that segregates for berry size and seedlessness.  In this talk we will specifically compare the kind of results obtained when using the Stacks and Tassel analysis pipelines on the same dataset.  Genotyping each parent multiple times is valuable depending on the scientific question / population structure and the quality of a reference genome can impact the results.  For typical QTL mapping a Stacks approach seems to work very well.  For genome wide association studies (GWAS) Tassel is more powerful.  The potential of combining the approaches will be discussed.