Session 2 - Variant calling analysis

Owned by Roberto Barrero Gumiel
Last updated: May 14, 2024
2 min read

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 : sarek: Introduction

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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:

 

Request Bioinformatics support:

 

 

 

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