I need to calculate number of different and effective allele for a diversity study using large SNP dataset. Normally I use GenAlex but I can't load the data due to limited no of columns. Please advise.
Kak su leh try Geneious Prime https://www.geneious.com/tutorials/map-to-reference/. Dia ada trial version. Saya tak pernah run for SNPs, tapi the tool is super user friendly and easy to understand to manage large NGS dataset.