Today’s overview:
Introduce Variant Calling analysis
Learn to install Nextflow
Test and run the nextflow nf-core/sarek pipeline in the HPC cluster using public data. Exercises include:
Exercise 1: Running a test to verify the execution of the pipeline
Exercise 2: Running the sarek variant calling pipeline with a family trio data (NA12878, NA12891, NA12892)
Exercise 3: Running the sarek variant calling pipeline with liver samples
Exercise 4: Use learned skills to prepare and run variant analysis for a second family trio (HG005, HG006, HG007)
Outputs: Review of variant calling results
Overview of downstream variant calling analysis using R (hands-on session will be on Session 5)
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.
