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ksiewert / BetaScan

Genome-wide scan for balancing selection using beta statistic
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How to calculate the theta and Watterson's theta? #15

Closed SC-Duan closed 2 years ago

SC-Duan commented 2 years ago

Hi, I'm trying to calculate B2 using Betascan. This needs the theta value as a parameter, and how should I calculate it based on vcf file or beta input file? if I set DivTime parameter, this also need the 4Neu in BALLET. Thank you!

ksiewert commented 2 years ago

Hello! If you're not comfortable estimating theta and the DivTime for your species isn't previously known, it might be worth just using the original Beta 1 statistic. That way you don't need theta or the DivTime. if you do really want to use B2, then I would get regions of the genome that you think are neutrally evolving, and calculate Watterson's theta on them.

SC-Duan commented 2 years ago

Thanks for your reply. I just want to test the B2 results and I request the source code from Achaz to calculate the theta and have not heard back yet. Are there some softs can do it? Thank you very much!