Genotype QC default setting

[gaow]

• Kinship coefficient for related individuals: 0.0625
• MAF designed for common variant analysis: 0.01 (although we will prepare both common and all variants data)
• Variant level missingness threshold: 0.1
• Sample level missingness threshold: 0.1
• LD pruning via PLINK for PCA analysis:
  • window 50
  • shift 10
  • r2 0.1

I believe these are widely accepted QC settings, although people might have different thoughts on what missingness threshold to set, eg
https://dx.doi.org/10.1002%2Fmpr.1608.