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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