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
library(devtools)
install_github("Displayr/flipPlots")- code usage with examples
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
- plink
- R/Shiny
- feature frequency profile
-
We downloaded binary plink files which has prefix of `cteam_extended.v4.maf0.1perc' which located on Simons Genome Diversity Project (SGDP) section I.
- Byung-Ju Kim (bjk@inu.ac.kr)
