PCA on genotype default setting

[gaow]

• MAF cutoff for PCA analysis: 0.05 -- we focus on very common variants
• Number of PCs to use for partial PC computation: 20
• Number of PCs based on which Mahalanobis distance should be computed: 5
• Mahalanobis distance based on mean or median: median
• Mahalanobis distance based cummulative probability cut off for outliers: 0.997
• Mahalanobis distance p-value cut off based on chisq distribution: 0.05