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chanjed / LDhelmet_parallel

parallel tempering of LDhelmet
GNU General Public License v3.0
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How to calculate population-scaled mutation rate ? #1

Open yuan102379 opened 4 years ago

yuan102379 commented 4 years ago

Hi @chanjed ,

LDHelemet could be a wonderful tool to estimate the fine-scale recombination rate.

I have read the mannual for several times. However, as a beginner, I meet with the problems about how to population-scaled mutation rate. The population-scaled mutation rate could be necessary for the accurate estimation of LDHelmet.

Could you give me some suggestions, please ?

Thanks a lot and look forward to your response.

Yours,

Yuan

chanjed commented 4 years ago

I'd recommend using: https://github.com/popgenmethods/pyrho rather than LDHelmet as it is faster and likely more accurate. Mutation rate estimation depends on the organism you are studying. For humans, ~1.1×10−8 per site per generation is widely accepted.

yuan102379 commented 4 years ago

Thanks chanjed @chanjed ，

In fact, it is a littile amazing that you recommed me to use another sofitware to calcualted fine-scale recombination rate. Now that, I would like to empoly both software and compare their results.

Thanks again.

Yours,

Yuan