FunGen-xQTL Resources

ADGC GWAS imputation protocol

This protocol is adapted from the ADGC GWAS Data QC Protocol. It generates imputed genotype data for xQTL analysis in some cohorts.
Cohort
AD GWAS
Modality
ProtocolGWAS
Release status
Stagednot yet verified
Lead analysts
Xuanhe ChenSelect a name to email them

Access

Access terms for this page are not set yet. See How to get the data.

Contact

Xuanhe Chen

Imputation by TOPMed imputation server

The TOPMed imputation server returns results on hg38.

  1. Register an account

  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”