Could anyone help me with an advice on how to quantify variant / clone enrichment in a given condition compared to another condition?
Example: let's say I have a cell line where a sub-population has a certain variant, and treat the cell line with a given drug. I do RNA-seq on several replicates of the cell line population before treatment and after treatment and call variants from these RNA-seq data. The allelic frequency of the variant is higher after treatment (i.e. the ratio of RNA-seq reads carrying that variant is higher in the post-treatment condition). Would the hypergeometric / Fisher's exact test be suitable to assess the significance of allele enrichment of the variant after treatment? Or would some other test be suitable instead?
Thanks for your answers!
