Related Issues (19)
- Don't remove msprime mutations in the recaptiation region HOT 3
- stats are being calculated from all individuals in tree sequence HOT 2
- ploidy being set as 1 HOT 2
- snakemake won't work for more than one param comb HOT 1
- convertToSubstitution=T? HOT 1
- reconciling rec map in hapmap with actual chr sizes HOT 4
- change default args in overlay.py
- handle the rescaling factor the same way stdpopsim does HOT 11
- make SLiM check if any intermediate tree seq has been saved - and restart from there HOT 3
- set simplification interval for high N sims HOT 1
- shifting coordinates in exon tsv
- a
- vectorized genomic elements HOT 1
- review union and tskit stats
- stats script should be aware of windowing during simulation step
- fix the way you do recapitation HOT 2
- rerun stats for the real data (update pxpy branch overlap figure)
- exons table in union_recap_mut.py includes exons in the padded region
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