I have a sample from a cultivated tetraploid (plant) and the reference genomes I am working with are the two diploid progenitors. I am running Basic Variant Detection on the sample against one of the diploid references and then I will run it against the other diploid.
Should the ploidy setting be 2 or 4? I thought it should be 2.
Should the ploidy setting be 2 or 4? I thought it should be 2.