Question: Can you use germline variation calling on a normal embryonic stem cell line?
1
gravatar for maria2019
15 months ago by
maria2019100
maria2019100 wrote:

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?

ADD COMMENTlink modified 15 months ago by Emily_Ensembl21k • written 15 months ago by maria2019100

I got the results that I should've gotten if I had a germ cell

What does that mean?

ADD REPLYlink written 15 months ago by ATpoint36k
6
gravatar for Emily_Ensembl
15 months ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

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.

ADD COMMENTlink written 15 months ago by Emily_Ensembl21k

Thank you very much Emiliy. This was SO helpful.

ADD REPLYlink written 15 months ago by maria2019100

If the answer resolved your question, you should mark it as accepted. You can accept more than one if they work. Upvote|Bookmark|Accept

ADD REPLYlink written 15 months ago by genomax85k
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