Other things I'd want in the pipeline if it were real data and I had more time

General

• check sequencing/genoyping platform and adjust QC accordingly

Sample QC/ Sample Selection

• X inbreeding - check for sample mix ups
• PCA for cryptic and divergent ancestry (and covariates in GWAS)
• test for duplicate samples
• HapMap concordance

Site QC

• some kind of depth filter
• filter on QUAL?

Regression

• include more rarer variants (Rare variation, common disease hypothesis)
• update method for regression to account for rare variants, covariates and family structure
• Covariates (assuming the phenotype is BMI or something similar): age, sex, socioeconmic background, chronic disease, [height?]

QQ

• Inflation - before and after QC
• Use genomic control method and calculate inflation factor

Other

• imputation