I have WES/WGS data on a normal embryonic stem cell line and I want to cell any possible variants in it. I worked with the GATK germline variation calling and I got the results that I should've gotten if I had a germ cell. Is that normal? Can you use germline variation calling on a normal embryonic stem cell line?
I think maybe you're confused about what is meant by "germline". When talking about "germline variant calling" we're not referring to the cell type, we're referring to where the variant came from. In this case "germline" means that the variant was inherited from a parent and should be found in every cell of the individual. This is opposite to "somatic" which means the mutation occurred somewhere in that individual's body and will be shared only by a small number of cells, often a tumour. The process of "germline variant calling" is, therefore, identifying all the variants in that individual that differ from the reference genome, and the process is identical whatever cell type you use for this.