Possible analysis from simplified VCF files

Question

[karolror]

During the studies, we were given the task of carrying out simple analyzes using simplified vcf files, which only contain chromosome numbers, identification numbers and genotypes; something like that:

Chr1 353 1/1 1/1 0/1 0/1...

Chr1 355 1/1 1/1 0/1 0/1...

and so on...

We were given two files - one with sick animals and one with healthy animals. What kind of comparison, analysis, testing can be done here and some conclusions can be drawn from it? It doesn't have to be anything complicated as this is the first project of its kind and its main goal is to focus on using parallel programming in R.

Answer 1

[4galaxy77]

I won't tell you exactly what to do, since it's better if you figure that out yourself. However, you could compare the allele frequencies between the sick and healthy animals to see if there are any SNPs which show extreme differentiation and thus may inform you about why the sick animals are sick.