I am trying to do whole genome phylogenomics of a dikaryotic fungus, however, I am confused about the reference used for the variant calling. We have a high quality, nearly phased genome of the fungus in the form of primary and alternate contigs. For the variation calling, I have used only the primary contigs as a reference, but the number of the variants called against the primary contigs are so high that I am finding it difficult to process them for subsequent analysis.
So I ran BUSCO analysis on the primary contigs and extracted the single copy BUSCO genes and used them as a reference for the variant calling. This has helped in reducing the total number of the variants considerably which is good but I don't know if this is the correct way of variant calling (using 1300 BUSCOs as reference for variant calling).
Thanks Ram
