I want to study the genetic diversity (SNP) in a population of nematodes (Caenorhabditis elegans). As the organism is small (less than 1 mm), we pool a lot of individuals to have enough DNA to prepare the libraries, we talk about PoolSeq. Another problem is that it is difficult to know the exact number of individuals placed in the pool, and thus ploidy.
I was wondering if Mutect2 could be adapted in this case, I assuming that searching for variants within a nematode population pooled could be similar to searching for variants among a cancer cell population.
I wanted to have your opinion on this approach, does it seem like a good idea to proceed this way?
Thank you !
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