SNP quality control and PCA analysis with Plink Software in RStudio.

PLINK command-line program, which easily handles large-scale SNP dataset. This software involve running several commands (or options), e.g. to produce summary statistics on missing data, to exclude some SNPs based on these results, to run an association analysis. Each command involves
a separate instantiation of plink – note that PLINK does not remember any parameter settings between different runs or store any other information. User must always check *.log file to get parameter settings.

In this tutorial, I have used Plink to perform SNP QC and to investigate population structure using PCA method. PCA plot was produced using ggplot2 R package.

Plink software:
https://www.cog-genomics.org/plink/1.9/

SNP QC using TASSEL software:
   • Genome-wide Association Study (GWAS) ...  

Covert genotypic data into different format:
   • Convert SNP data from one format to a...  

GWAS analysis:
   • GWAS analysis using rMVP package in R...  


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