Population structure analysis pipeline

A pipeline using SNP variant information to conduct population structure analysis.

Dependent software/script

• PLINK1.9
• VCF2PCACluster
• ADMIXTURE
• FastTree
• VCFtools
• bgzip (part of htslib)
• vcf2phylip

What to input

Just vcf file containing your population variant information in compressed format (vcf.gz).

Since ADMIXTURE only accpets vcf file with integer format chromosome ID (e.g. 01 for Chr01), please remember to modify your vcf file.

What the pipeline does

• SNP filtered all missing site
• SNP vcf convert to plink format
• SNP pruned according to LD block
• PCA cluster
• ADMIXTURE analysis
• Phylogenic tree construction

What to output

• PCA eigen principle component file used for PCA plot
• Tree file in nwk format
• ADMIXTURE Q file and P file