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
Overview of the Nextflow nf-core/sarek variant calling pipeline
Source : https://nf-co.re/sarek/3.2.3
The sarek pipeline is designed to screen for inherited germline or somatic mutations in samples for which there is a reference genome sequence.
