Learn how to create and run your own target discovery pipeline with GWAS and PheWAS. This webinar shows an end-to-end target discovery pipeline run entirely on UKB RAP that you will be able to replicate for your own research projects on the platform.
Learn how to:
-Extract data using dx extract_dataset
-Make sample and variant QC
-Run GWAS analysis using REGENIE app
-Perform LD clumping using PLINK to cluster significant GWAS variants
-Run PheWAS analysis
As this is an advanced webinar, we expect that audience has experience with:
-Performing analysis on UKB RAP
-Running JupyterLab on UKB RAP
-Compiling and running WDL workflow
-Running SAK using GUI or CLI
00:00 Introduction to Genomics-based Target Discovery
06:20 Step 1: Creating Cohorts
08:22 Step 2: Extract sample phenotype data
10:47 Step 3: Lift over array data
13:46 Step 4: QC Sample sample phenotype data
16:20 Step 5: QC array and impute data
19:49 Step 6: GWAS
24:56 Step 7: LD Clumping
29:16 Step 8: PheWAS
35:31 Conclusion
38:12 Q&A
Негізгі бет Ғылым және технология End to End Target Discovery with GWAS and PheWAS on the UK Biobank Research Analysis Platform
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