Downstream analysis of VCF file

Question

[javanokendo]

I have a VCF files which I would like to do all downstream analysis such as Structure, PCA, Linear Discriminant Analysis. Can I get some pointers to the best R packages to do this since I am moving into this field and I really need some assistance.

[Friederike]

What types of questions are you trying to assess? That will drive the types of packages and analyses that may be useful for you. Have you tried any packages yet and found them lacking?

This may be a start, it was the first hit I got when I searched for "R package vcf file analysis": https://jnmaloof.github.io/BIS180L_web/2021/05/13/R-SNPs/

Answer 1

[abedkurdi10]

BCFtools is a great tool to perform a lot of analyses on VCF files. For example, you can use bcftools query module to extract tabulated format of the genotypes and you can run principal component analysis on them. Another example, if you want to compare vcf files, what are the common mutation, what are the unique mutations for each case, you can use bcftools isec module. BCFtools has a lot of modules, it is worth checking it.