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Today’s overview:
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:
Exercise 1: Running a test to verify the execution of the pipeline
Exercise 2: Running the sarek variant calling pipeline with a HapMap 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
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Exercises:
Request Bioinformatics support:
eResearch portal: https://eresearchqut.atlassian.net/servicedesk/customer/portals