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Aims

• Introduce Variant Calling analysis

• Learn to install Nextflow

• Test the execution of the nf-core/sarek pipeline using test data

• Run the nf-core/sarek pipeline using real public data including family trio(s) and liver samples

• Evaluate the output of variant calling and annotation

• Overview of downstream variant calling analysis using R (hands-on session will be on Session 5)

• Test and run the nextflow nf-core/sarek pipeline in the HPC cluster using public data. Exercises include:

  • Running a test to verify the execution of the pipeline

  • Running the sarek variant calling pipeline with a HapMap trio data

  • Running the sarek variant calling pipeline with liver samples

Introduction

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• Installing Nextflow

• Exercise 1 - test

• Exercise 2 - trio

• Exercise 3 - liver

• Exercise 4 - trio 2