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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.
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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.
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