VCF Filtering and PCA

Download VCF File

Download the VCF file to be used from this link: Zenodo Dataset

Filtering and Analysis Steps

• Apply base quality, genotype quality, and Hardy-Weinberg Equilibrium (HWE) filters
• Remove Indels
• Apply the individual missingness filter
• Remove individuals with missing proportion greater than 60%
• Apply a missingness filter to keep variants common among a proportion of individuals
• Extract the number of variants remaining upon applying missingness filters from 0.1 to 0.9 and save to a .txt file
• Plot the data in variant_counts.txt using ggplot2
• Apply max missing 0.6 filter (retain variants with at least 60% data)
• Use site mean depth filter to obtain mean depth at each variant site
• Find the percentile depth between 0.05 and 0.975 (middle 95 percentile)
• Apply filters to keep only variants with depth values lying in this range
• Perform PCA (Principal Component Analysis)