Clarity on reading recombination map correctly

[Miguel Guardado]

Hello!  

I have a quick question about correctly using the recombination map feature.

I am working with a recombination map from Halldorsson et al 2019 where rates are reported in cM/Mb. My understanding is that SLiM expects recombination rates per base pair, so I would need to convert cM/Mb to per-bp units (i.e., multiply by 1e-8). Is that correct?

Note, I am currently using SLiM v4, as I have not yet updated py_ped_sim to v5. Im not sure if using v5 would alleviate this in any way. 

Thank you for your time, and I appreciate all the work that goes into SLiM!!

[Peter Ralph]

That's correct: multiply by 1e-8 to get to recombinations per bp. (Also, make sure to carefully read the documentation around endpoints.)

Happy SLiMulating!

---

From: slim-d...@googlegroups.com <slim-d...@googlegroups.com> on behalf of Miguel Guardado <guardado...@gmail.com>
Sent: Thursday, April 16, 2026 12:28 PM
To: slim-discuss <slim-d...@googlegroups.com>
Subject: Clarity on reading recombination map correctly

 

Hello!   I have a quick question about correctly using the recombination map feature. I am working with a recombination map from Halldorsson et al 2019 where rates are reported in cM/Mb. My understanding is that SLiM expects recombination rates

ZjQcmQRYFpfptBannerStart

You haven't previously corresponded with this sender.

Use caution with links and attachments. Learn more about this email warning tag.

Report Suspicious

 

ZjQcmQRYFpfptBannerEnd

--
SLiM forward genetic simulation: http://messerlab.org/slim/
---
You received this message because you are subscribed to the Google Groups "slim-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to slim-discuss...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/slim-discuss/05e0496e-7d11-4683-8730-14ff76d989b7n%40googlegroups.com.

[Ben Haller]

Hi Miguel!  SLiM expects recombination rates per-base-pair, yes.  The manual states, in a couple of places, things like "Recombination also occurs uniformly at a rate of 10-8 per bp per gamete (corresponding to 1 cM/Mbp)", so if that corresponds to what you're saying, then it sounds like you've got the correct conversion factor.  :->  No, SLiM 5 doesn't change this picture at all.  Happy modeling!

Cheers,
-B.