Principal component analysis for microbial SNP

Question

[Bioblazer]

I have 7 different geographical location isolates of mycobacterium SNP dataset in seperate VCF files. I want to perform PCA analysis. Tutorials are available for biallelic data or multiallelic data. What are ways for doing PCA for haploid ? From my understanding , I think I should merge VCF files into single file for analysis if it so what are tools are available for merge the data?

Answer 1

[Kevin Blighe]

You can use BCFtools to merge your VCFs, and then PLINK to perform PCA using the genetic information contained within them. I have done this previously with 1000 Genomes VCFs: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2