Postdoc Jacob Landis presented a SNP calling webinar with CyVerse on Friday September 11th. Slides and associated tutorials for both command line and point-and-click Discovery Environment are available on GitHub: https://github.com/bcbc-group/CyVerese_SNP_calling_webinar
The webinar covered SNP calling using RAD-Seq data with both a de novo and reference based approach, as well as using GATK to call SNPs from other forms of genomic data. Filtering VCF files was also briefly included.
There may be a followup webinar in the Spring covering downstream analyses.