ARGsims

Code and simulated data used for the paper "Evaluation of methods for estimating coalescence times using ancestral recombination graphs" https://www.biorxiv.org/content/10.1101/2021.11.15.468686v4

trees

tree sequences simulated with msprime (only the ones within github file size limit)

vcf

vcf files simulated with msprime (only the ones within github file size limit)

scripts

Simulations

Scripts for msprime simulations:

• 1_msprime_sim.py Simulations with msprime

• 2_msprimefinitesites.py Add mutations under JC finite sites model to previously simulated trees

Other general scripts

• calc_kld_ranks.R calculate KLD from ranks distributions
• plot_ranks.R plot distribution of ranks
• organizeQuantileOutput get counts of ranks

ARGweaver scripts (in scripts/argweaver)

• 2_vcf2sites.py convert vcf to ARGweaver sites input format

• 3_run_argweaver_smcprime_hudsim.sh run ARGweaver

• 4_arg-summarize2plot_allchunks.sh summarize args to extract pw coalescence times and call plotting scripts:

  • coalTimeRank.py get ranks of coalescence times
  • getPostMean_bedmap.sh get point estimates of coalescence times (mean of the posterior) and match to true (simulated) values
  • MSPcoalTime2bed convert coalescence times from msprime to bed format
  • plot_pointestimates.R plot heatmaps of point estimates (estimated vs. simulated)
  • plotTc_argw.R plot distribution of coalescence times

• 5_pointestimates.sh plot point estimates of coalescence times

Relate scripts (in scripts/relate)

• 2_run_relate2plots.sh run Relate, extract pw coalescence times and call all plotting scripts:

  • outputCoalTime output pairwise coalescence times from anc/mut files
  • plot_pointest.R plot point estimates
  • plotTc_relate.R plot distribution of coalescence times
  • thin.R thin MCMC samples

• recombination maps: sim_std.map, sim_r2e7.map, sim_r2e9.map

Tsinfer+tsdate scripts (in scripts/tsinferdate)

• 2_tsinfer_date.py run tsinfer+tsdate
• 3_organizeTc.sh match simulated to estimated coal times
• 4_plot_pointestimates_tsinfer.R plot point estimates of coalescence times
• 5_plotTc_tsdate.R plot distribution of all pairwise coalescence times