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01_Quality_Control
- This process can be divided into 2 parts including individuals level and variant level
- In each step, only low quality sample and variant will be excluded.
- population stratification and relatedness is ignored in this step because GRS exploration will not be afftected by these concerns.
- This process can be divided into 2 parts including individuals level and variant level
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02_Genotype_imputation
- The genotype of RIKEN I and II will be imputed by using 1000 genome project phase I as reference in order to capture all SNPs in the summary statistics.
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03_Statistical_Analysis
- There are two main parts including Exploring GRS distribution in five NCDs and evaluating weighting straties (weighted genetic risk score and unweighted genetic risk score)
- All graph are plotted by using Rscript
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QC Workflow and Visualization for Genotype Data
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