Comments (4)
Seems like you should set the chromosome length to the last position in the map?
from greatapes_sims.
That's what I was doing before. But then it will be different than what is seen in the actual data and in the annotations.
The chunk that is missing is from the map is ~500kb for each chr.
from greatapes_sims.
Ok, but then maybe you should not use that bit of the real data, either? Unless we really think that 500Kb actually has no recombination.
from greatapes_sims.
Ok, changed to get chr lens from the rec map! Thanks.
from greatapes_sims.
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
- 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
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- fix the way you do recapitation HOT 2
- specifying more than one replicate per parameter combo will break things
- 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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