Open grcvhon opened 1 year ago
Hello Vhon, Can you attach your par, est, tpl and one or more SFS files? I will be very busy next week, so will try to look at this then.
Thanks Isaac!
I have attached the files and also provide description for each in README.txt (included in the zip file). git-bootstrap_fsc.zip
The ways I've tried non-parametric bootstrapping to obtain 95%CI included:
1) simulating 100 SFSs then performing 20 independent runs
(using -n
coalescent simulations and -L
optimisation cycles: -n1000000 -L100
and
-n100000 -L30
[this one is mainly to speed up and from fsc27 manual too])
2) simulating 100 SFSs, supplying --initValues file.pv
(as in fsc27 manual), then performing 20 independent runs
3) simulating 1000 SFSs and running fsc2 with --initValues file.pv
But for some reason, my point estimates are always outside of the 95%CI. For example: Point estimate for effective population size parameter SEMP = 644,356 95%CI obtained using bootstrapping number (2) above: 659,668.4 - 681,601.9
Many thanks again!
Hi Isaac,
I am having an issue about bootstrapping in fastsimcoal2 and appears that my point estimates fall outside 95% confidence intervals.
I have tried non-parametric bootstrapping by sampling with replacement my VCF (thanks for the modifications in the easySFS.py script specifically
--resample-vcf
) but after many attempts, my point estimates from observed data still fall outside the 95%CIs.I may be doing something that's totally wrong and would like to use your fsc2_scripts for bootstrapping however I was having difficulty interpreting how to use them. I was hoping if you could give some direction.
Thanks so much!
-Vhon