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”