I would like to identify the somatic mutations present in a cell line and characterise the genes that are potentially affected by those mutations. For example, are there oncogenes mutated in a subpopulation in the cell line?
I have currently access to single cell WGS data and sequencing data of the bulk sample derived from the same clone. The data was generate after MDA amplification of the single cell's genome so I am currently evaluating SCCaller and Prosolo for variant calling. If I correctly understand single cell variant calling, mutations called in each cell are called relatively to the bulk background sample. So each cell separately doesn't provide much information on the cell line itself.
My questions are:
- Do i need single cell WGS to quantify the overall 'genomic health' of a cell line or can I just use deep sequencing followed by somatic variant calling against a reference genome.
- What added value can single cell WGS provide here and how can I extract that information?
Links to papers, packages or statistical models more than welcome.