Variant Analysis Task List

Task 1: VCF to PLINK Format Conversion

Convert VCF to PLINK binary format using plink --make-bed
Edit .fam file to add region information to second column
Edit .bim file: Replace chromosome name E2 with 1

Task 2: Principal Component Analysis (PCA)

Run PCA with plink --pca 5
Visualize in R with ggplot2
Save PCA plot as .png and .pdf

Task 3: File Transfer

Use scp to copy output files from server to local machine
Example: scp user@IP:path/to/Rplots.pdf .

Task 4: ADMIXTURE Analysis

Create conda environment and install ADMIXTURE
Run ADMIXTURE for K = 2 to 4 using loop
Generate output files .K.P and .K.Q

Task 5: ADMIXTURE Plotting

Read .Q and .fam files into R
Extract group/population from sample IDs
Reshape data and plot using ggplot2
Save barplot as admixture_K3_grouped.png

Task 6: Heterozygosity Estimation

Install rtg-tools using conda
Run rtg vcfstats on final VCF
Save output as .vcfstats file

Task 7: Optional / Miscellaneous Tasks

Activate/deactivate conda environments as needed
Exit server after analysis with exit command