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Polygenic adaptation to optimum shifts

Validation of simulation (additive model)

Under certain conditions, the expectation of VG is 4muVS. These sims check that the code is giving that.

To run:

qsub hpc/validate_additive.sh
#Wait a while
python python process_validate_additive_output.py -i popstats.h5 -o popstats.csv
R --no-save --args popstats.csv popstats.pdf < Rscripts/plot_validate_H2_output.R

TODO

  • How does $\sigma_\mu$ affect things?
  • I should probably do a "track everything" simulation, so that I can track pop-gen stats for interesting replicates. Alternately, I should require that the tracking API use a diferernt RNG, which is probably way more efficient. How, though, w/o breaking things?
  • How does linkage affect things?
  • TFL2013/GBR model

The question of linkage

The latter should be done via fwdpp's multi-locus API:

  • The total mutation rate is $\mu$
  • There are $k$ regions, each with mutation rate such that $\sum_i \mu_i = \mu$.
  • Each has a within-region recombination rate
  • Each has a within-region neutral mutation rate
  • The within-region rates should be set to model a 100kb "human" region, b/c that'll give a lot of neutral SNPs to sample
  • Vary linkage amongst regions -- 0.1, 0.25, 0.5
  • Track everything--samples and mutation frequncies.