Session 2 - Variant calling analysis

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

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Overview of the Nextflow nf-core/sarek variant calling pipeline

Source : https://nf-co.re/sarek/3.2.3

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The sarek pipeline is designed to screen for inherited germline or somatic mutations in samples for which there is a reference genome sequence.

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Exercises:

• Installing Nextflow

• Exercise 1 - sarek test

• Exercise 2 - trio case study

• Exercise 3 - liver case study

• Exercise 4 - Personal Genome Project - Han Chinese family trio

Request Bioinformatics support:

• eResearch portal: https://eresearchqut.atlassian.net/servicedesk/customer/portals