Using a full publicly available chromosome read-set from one of the 1000 genome samples:

​Perform a complete analysis workflow including QC, read mapping, read coverage analysis, and variant calling against the human reference genome.
Use GenePattern and open source software to evaluate each step of a classical NGS variant workflow and feel the complexity of the task.
Quickly compare the obtained results with gold standard public data

The skills acquired during this session should allow participants understand what variant calling implies.

Participants with experience in command line can do the workflow using command line tools.