Practise Datasets (NGS & GWAS)

sample set of fastq files with paired end reads

A set of fastq files from a tumour/normal pair

A bed file with positions of UCSC hg19 known genes (including gene symbols)


GWAS datasets

Data Format

small dataset: Tutorial_PLINKsmall

Large dataset: Tutorial_PLINK

Quality Control Datasets

Protocol: GWAS Quality Control Practical Session

  1. Create a folder in your home directory – called GWAS
  2. Create subfolders called data, codes, QC, AssociationAnalyses
  3. Move to ‘data’ subfolder
  4. Download gwas data: wget
  5. Unpack the data: tar -xzvf GWAS_practical_1.tar.gz


Basic analysis of genome-wide association studies

Protocol: Basic analysis of genome-wide association studies


gPLINKGWAS Tutorial with PLINK




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