ADGC GWAS imputation protocol

ADGC GWAS imputation protocol #

Adapted from ADGC GWAS Data QC Protocol to generate imputed genotype data for xQTL analysis in some cohorts.

Contact #

Xuanhe Chen

Imputation by

TOPMed imputation server #

Note that results from TOPMed imputation server are all against HG38.

  1. Register an account (link)[https://imputation.biodatacatalyst.nhlbi.nih.gov/index.html#!pages/register]
  2. Log in
  3. Click “Run” and “Genotype Imputation (Minimac4)”
  4. Fill out the form 4.1. Name: Assign a job name 4.2. Reference panel: TOPMed r2 4.3. Input Files: File Upload 4.4. Array Build: GRCh37/hg19 4.5. Rsq Filter: Off 4.6. Phasing: Eagle v2.4 (unphased input) 4.7. QC Frequency Check: keep – select an option – 4.8. Mode: Quality Control & Imputation 4.9. Check “I will not attempt to re-identify or contact research participants.” 4.10. Check “I will report any inadvertent data release, security breach or other data management incident of which I become aware.” 4.11. Click “Submit Job”