Adam Auton

Some thoughts below; although I will caution that it has been many years since I have thought about these issues. > > 1.can i use summary.txt to draw the results...

This looks somewhat more discordant than I would expect. What parameters are you using? I also note that the units on the y-axis appear different. On Sun, 5 Jun 2022...

For starters, I suggest converting the interval output to rho / kb (i.e. scaling by physical distance, in kb, between SNPs), which may resolve some of the discrepancies. I'd also...

Thank you - it is a good suggestion. However, it would (I think) break backwards compatibility with older versions. I’ll think about it - maybe there is a way to...

Depending on your exact situation, one suggestion would be to estimate recombination results using a range of (reasonable) theta estimates. My expectation is that the results should be qualitatively similar....

When faced with this problem a long time ago, I believe we just used the female individuals to estimate recombination rates. Treating the males as diploid will likely lead to...

Vicencio, A few thoughts: - Running across populations is not ideal, as the LD structure could be influenced by population structure. LDhat assumes your data comes from a homogenous population....