I want to do one PCA analysis with some second-hand SNP data, however, all the data I have are the info about " Chrom, POS, REF, ALT".
I've learned the program of PCA plot with the raw sequencing output vcf file, but, in my case, I do not have that kind of file.
then may I ask you whether I can do the PCA analysis with my current data?
thanks a lot.
You need the genotypes of the variant sites in order to do a PCA. One of the ways to perform PCA from a VCF file is using plink: https://www.cog-genomics.org/plink/1.9/strat#pca. You obtain the .eigenvec file which you can plot using ggplot in R or using some other package.
Since you do not have access to a VCF file, it may be difficult to perform PCA with the data you currently have as you don't have any quantitative value describing the SNPs (except the SNP position which is not helpful for PCA).
