PSMC analysis: input data processing, mutation rate, generation time

Question

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Hi Everybody,

I have few questions regarding PSMC analysis, can anyone please guide me..

1. What are the general masking filters that would be applied during input files processing in PSMC analysis for reliable results, and how to apply them?

2. During plotting PSMC plot construction, how to decide the mutation rate (mu) and generation time.. I have seen in different publications various parameters are used.. can anyone please guide about the most accepted one in current population genomic research? and what are the considerations while choosing fast and slow mutation rates?

Thanks a lot in advance!