[sfscode-users] Variation in cross-over rate

[Rémi Matthey-D. <ma...@zo...>]

Hi all,

*Goal*

I am trying to simulate 3 unlinked *groups* of 5 linked *loci *each (for a
total of 15 loci). Cross-overs occur within each group and its rate varies
from group to group. Annotation (coding/non-coding and selection
coefficients) varies from locus to locus.

*Why I am getting confused*

I can indicate the genetic distance between loci with *--linkage. *However,
when annotating with a file (*-a F annotate.txt*), one must indicate the
physical distance, which entries will, I suppose, play out with the map
file (*-r F map.txt*) in order to calculate the genetic distance. If this
is true it means that the *--linkage* command is then ignored. If I
understand correctly using *-a F annotate.txt *necessarily causes SFS_CODE
to not consider *--linkage*. Now, the issue is that in the map file (*-r F
map.txt*), I think it is impossible to indicate several unlinked loci.

*Question*

Can you help me with that by sending me a minimalist code line and file
example that would make the simulation I am trying to have?

Thanks a lot for your help.

Remi

-- 
Remi Matthey-Doret
   www.zoology.ubc.ca/~matthey/
    PhD Candidate, M. Whitlock Lab
    Beaty Biodiversity Research Center, room 250
    Dept. of Zoology, University of British Columbia
    6270 University Blvd, Vancouver, BC, V6T 1Z4
    @RemiMD
    Phone: (604) 369-5929