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Calculate quanitles of expected S*

sstar provides a function quantile to estimate different quantiles of expected S* scores from simualted data without introgression. If users need to estimate quantiles of expected S* with large scale simulation, we recommend users follow our sstar pipelines in sstar-analysis, for example, sstar.snake.

Input

Users need to install the ms program from Hudson Lab and provide a demographic model (e.g. BonoboGhost_4K19_no_introgression.yaml) in Demes YAML format. Then users can use the following command:

sstar quantile --model BonoboGhost_4K19_no_introgression.yaml --ms-dir ./msdir/ --N0 1000 --nsamp 22 --nreps 20000 --ref-index 4 --ref-size 20 --tgt-index 3 --tgt-size 2 --mut-rate 1.2e-8 --rec-rate 0.7e-8 --seq-len 40000 --snp-num-range 25 30 5 --output-dir quantiles --thread 2

The meaning of each option can be found using sstar quantile -h.

The expected result above can be found in test.quantile.exp.summary.

Output

An example for the output is below:

S*_score SNP_num quantile log(local_recomb_rate)
62168.0 25 0.5 -8.154901959985743

The meaning of each column:

  • The S*_score column is the S* score.
  • The SNP_number column is the number of SNPs.
  • The quantile column is the quantile of the expected S*_score in the simulated dataset.
  • The rec_rate column is the logarithm of the local recombination rate.