Hi Moritz, For a quick breakdown of a variant pipeline, this recent workshop has slides. Basically you map (BWA is a good choice), choose a variant caller (Freebayes or other), and look at associated annotation ( SnpEff): http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay#Variant_and_S NP_Analysis_with_Galaxy Tools in the group "NGS: QC and manipulation" such as FastQC should be able to help with quality checks and then others in same group with manipulations. For the detailed steps of sorting out known SNPs, synomymous vs non-synonymous, etc, you have a few choices. The tools in the groups ' NGS: GATK Tools (beta)', ' Phenotype Association', and 'Genome Diversity' are the places to look. Tools have help on the forms, including links to publications. Or you can look in the tool shed for more choices to use in your local instance: http://toolshed.g2.bx.psu.edu/ If the data in the shared link is really patient data that is protection sensitive, I would recommend unsharing the history and deleting the data permanently from the public Main Galaxy instance. Good luck with your thesis! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org