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https://github.com/ahmedmoustafa/genetic-ancestry

Genetic Ancestry

https://github.com/ahmedmoustafa/genetic-ancestry

Science Score: 13.0%

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Keywords

ancestry diversity ethnicity-analysis genomics ggplot pca plink population-genetics population-structure principal-component-analysis single-nucleotide-polymorphisms
Last synced: 5 months ago · JSON representation

Repository

Genetic Ancestry

Basic Info
  • Host: GitHub
  • Owner: ahmedmoustafa
  • License: cc0-1.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 13.9 MB
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  • Stars: 1
  • Watchers: 2
  • Forks: 0
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Topics
ancestry diversity ethnicity-analysis genomics ggplot pca plink population-genetics population-structure principal-component-analysis single-nucleotide-polymorphisms
Created over 2 years ago · Last pushed about 1 year ago
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Readme License

README.html 














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Genetic Ancestry


Ethnic Groups
Image source: Council
of State Archivists


A detailed workflow to compute and visualize the principal component
analysis (PCA) of genotypic Single Nucleotide Polymorphisms (SNPs). The
workflow leverages a curated set of 10,000 SNPs predefined by GRAF
to pinpoint ancestry markers. For the computation of PCA, we employ PLINK for generating the
eigenvectors and eigenvalues.




Workflow Overview


    

  1. Fingerprinting SNPs
Extraction: Extract GRAF’s 10,000 curated SNPs from the
dbSNP database.
    2. 

  2. Data Cleaning: Ensure the extracted SNPs are
exclusively biallelic. (included in the previous notebook)
    3. 

  3. SNPs
Retrieval from 1,000 Genomes Project: Extract the genotypes
of 10,000 fingerprinting positions from the 1,000 Genomes Project’s VCF
dataset.
    4. 

  4. PCA
Computation: Generate PCA’s eigenvectors and eigenvalues
using PLINK.
    5. 

  5. PCA Visualization:
Visualize the PCA data, highlighting the relationships between samples
using R.
    6. 






Populations PCA

Owner

  • Name: Ahmed Moustafa
  • Login: ahmedmoustafa
  • Kind: user
  • Location: Egypt
  • Company: American University in Cairo

Bioinformatics and Genomics Data Scientist

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