A pipeline using SNP variant information to conduct population structure analysis.
- PLINK1.9
- VCF2PCACluster
- ADMIXTURE
- FastTree
- VCFtools
- bgzip
- vcf2phylip
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.
- SNP vcf convert to plink format
- SNP pruned according to LD block
- PCA cluster
- ADMIXTURE analysis
- Phylogenic tree construction
- PCA eigen principle component file (used for PCA plot)
- Tree file in nwk format
- ADMIXTURE Q file and P file