This is a repository for the genome wide association study (GWAS) protocol I made during my MSc program at McMaster University, in Dr. Jianping Xu's lab (University Profile, Lab Website).

This github repository was written to submit to the BIO722 (Introduction to Bioinformatic Methods) graduate course at McMaster University and thus only uses a subset of samples and was conducted on a cluster.

This protocol was used as the foundation for three of my published papers ^{1, 2, 3} and for a poster presented at the 31st Fungal Genetics Conference. The poster, titled "Genomic and Genetic Analyses of Antifungal Drug Resistance in Aspergillus fumigatus" was presented by my supervisor Dr. Jianping Xu; Its contents were based on my thesis and I was responsible for drafting the poster's contents & layout.

1. Whole Genome Sequences
2. Quality Control and Trimming
3. Alignment and Variant Calling
4. Quality Control and Prep for Association Analysis
5. GWAS with Plink and Tassel
6. Visualization of GWAS Results
7. SNP Annotation