Genomic demography of world’s ethnic populations and genomic identity between two individuals

Introduction

This repository contains R/perl codes to conduct an analysis of the Genomic demography of world’s ethnic populations and genomic identity between two individuals and details

• current status : Code cleaning and review.
• sorry for the inconvenient We will upload the clean codes as soon as possible

Installation & functions

library(devtools)
install_github("Displayr/flipPlots")

code usage

• code usage with examples

workflow

graph TD
    A[fa:fa-database 1KGP]  --> |Phase 3 vcf  | C
    B[fa:fa-database SGDP]  --> |Plink files | C
    C[fa:fa-filter QC/QA] --> | 10-letter <br> encoding | D 
    D[Feature Profiling/Normalization] --> F 
    F[pairwise-JS divergence calculation] --> G
    G[BioNJ] --> | Tree Optimization by finding best K-mer | H
    A --> I
    B --> I
    I[meta data] --> J
    H[Final Tree] --> K[Sample Mapping]
    J[Map] --> K
    C --> L 
    L[pairwise IBS2 <br> calculation] --> M
    M[distance comparison] --> H

softwares used.

• plink
• R/Shiny
• feature frequency profile

DATA

• We downloaded binary plink files which has prefix of `cteam_extended.v4.maf0.1perc' which located on Simons Genome Diversity Project (SGDP) section I.

  • .bim.zip
  • .bed
  • .fam
  • metadata file was curated by BJK after download.
    • metadata manipulation

• 1000 genome project phase 3

custom functions to use

Contributers

• Byung-Ju Kim (bjk@inu.ac.kr)