Tutorial 03 - Pyseer Tutorial

This tutorial automates and reproduces the results from the penicillin resistance GWAS written by the pyseer authors.

  1. Download the tutorial data.

    git clone --depth 1 https://github.com/phac-nml/pangwas.git
cd pangwas

  2. Decompress the data.

    gunzip data/tutorial_core/snps.Rtab.gz
gunzip data/tutorial_pangenome/variants.Rtab.gz
gunzip data/tutorial_pangenome/clusters.tsv.gz

  3. Run the core genome GWAS on pencillin resistance.

    nextflow run phac-nml/pangwas -profile tutorial_core

  4. Open up the manhattan plot in Edge or Firefox.

    • Path: results/tutorial_core/manhattan/penicillin/penicillin.plot.svg
    • Hover your mouse over variants to see contextual information.

  5. Run the pangenome GWAS on penicillin resistance.

    nextflow run phac-nml/pangwas -profile tutorial_pangenome

Penicillin resistance is primarily controlled by core genome genes, and we can see that the major genes are identical between a pangenome and core genome GWAS.

The following image was made by importing the raw SVG plots into a vector graphics program (ex. Affinity) and adding text and box overlays to highlight the significant variants.