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QC Workflow and Visualization for Genotype Data

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The QC steps can be categorized into 3 parts

  • 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.
  • 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.
  • 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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