Will this method for genomic population structure analysis with VCF file help good for my work?
I was finding method for handling multi-calling VCF file and convert format for analyzing population genomics for fungi, which means dividing species or strains by genotype difference. So I found this site's instruction.
https://speciationgenomics.github.io/pca/
In this manual, they just simply run plink with VCF file and produce eigenval and eigenvec files. These two files make PCA plot with R.
plink --vcf $VCF --double-id --allow-extra-chr --set-missing-var-ids @:# \
--extract cichlids.prune.in \
--make-bed --pca --out cichlids
Does this simple method has no problem with analyzing population genomics and PCA visualizing with fungal multi-calling VCF files?
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