From d733a60f5cac1080c412f551d76897becc1e302d Mon Sep 17 00:00:00 2001 From: peter Date: Tue, 25 Sep 2018 09:07:17 -0700 Subject: [PATCH] added gotchas --- README.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/README.md b/README.md index b28b1ef0..b1f492c2 100644 --- a/README.md +++ b/README.md @@ -156,6 +156,26 @@ for ind in pyslim.extract_individual_metadata(mod_ts.tables): mod_ts.dump("modified_ts.trees") ``` +# Gotchas + +Here are some things that you currently **cannot** do with `msprime` and `SLiM`. +They are all on our list to enable; but if you need something for your workflow +and would like to contribute, please open an issue to discuss. + +1. You cannot generate mutations in `msprime`, and then use the tree sequence + to initialize a SLiM simulation. This is because SLiM requires mutations + to occur at integer positions, and `msprime` currently only generates + mutations under the infinite-sites model. + +2. You cannot use `msprime` to recapitate a SLiM simulation using a recombination + map that is not uniform. This is because `msprime` and SLiM both use discrete + recombination maps, but SLiM is discrete in physical coordinates (base pairs), + while `msprime` is discrete in genetic map units. You *can* run a simulation in + SLiM using any recombination map you want, and then recapitate using a uniform + map in `msprime` (this is the default). See [the msprime documentation](https://msprime.readthedocs.io/en/latest/api.html#initialising-simulations-from-a-tree-sequence) + for more discussion of recapitation. + + # Documentation Here we describe the technical details.