This workshop will focuss on the core steps involved in calling variants with the Broad Institute's Genome Analysis Toolkit (GATK), using the "Best Practices" developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. This course is organized in collaboration with Doc­toral Pro­gramme in In­teg­rat­ive Life Science (ILS)  of University of Helsinki.

This workshop highlights key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, RNAseq­ specific processing, and new somatic variant discovery capabilities in GATK4. It also mentions the use of pipelining tools to assemble and execute GATK workflows.

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non­human data, and we will address some questions regarding adaptations that are needed for analysis of non­-human data, but we will not go into much detail on those points.

Learning objectives

After this course you should be able to:

• Understand the overall variant discovery workflow rationale and requirements

• Understand key methods and functionalities in light of the latest research

• Understand key differences between germline and somatic variant discovery approaches

• Apply analysis tools and Best Practices workflows to a real data set

• Interpret analysis results and troubleshoot common problems

Aims

During this course you will learn about:

• Preprocessing of high-throughput DNA- and RNA-seq data

• Variant discovery (germline and somatic short variants, somatic CNV)

• Germline variant filtering and evaluation