Last updated: 2019-12-06

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Knit directory: PSYMETAB/

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Rmd 487b5f5 Sjaarda Jennifer Lynn 2019-12-06 update website, add qc description

The following document outlines and summarizes the quality control and processing procedure that was followed to create a clean, imputed dataset.

Quality control steps

results are saved to analysis/QC

  1. Preprocessing
  2. Strand alignment
  3. MAF zero
  4. Missingness
  5. Sex check
  6. Imputation (preparation and run)
  7. Run and download imputation
  8. Check imputation
  9. PLINK conversion
  10. Extract typed SNPs
  11. Merge imputed SNPs
  12. Relatedness
  13. Ethnicty check and admixture estimation
  14. HWE check
  15. MAF check
  16. Final processing

Results