Windows of equal recombination along the genome

[Luker121]

Hi,
I have a question regarding the utilization of MSMC2 for inferring windows of equal recombination rates along the genome.

My query pertains to the feasibility of using MSMC2 to infer segments of the genome where recombination rates remain consistent. Essentially, I am interested in identifying contiguous blocks of equal recombination rates for each haplotype segment.

Given that MSMC2 inherently performs calculations related to recombination rates, it would seem plausible that this information could be derived from the tool's outputs.

I would greatly appreciate any insights or guidance on this matter. If MSMC2 does indeed have the ability to provide such information, any pointers on how to extract or interpret this data would be immensely helpful.

Thank you in advance for your assistance and expertise.

[stschiff]

Hi. Well, MSMC2 can fit a single global recombination rate, but not variable per genomic region. So I think what you describe wouldn't be possible.