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popgenmethods / momi2

Infer demographic history with the Moran model
GNU General Public License v3.0
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No BED provided, will need to specify length manually with mutation rate #65

Closed XiaXiaTianTian closed 1 year ago

XiaXiaTianTian commented 1 year ago

Hi all, When I use /ds3200_1/proc/anaconda3/bin/python -m momi.read_vcf --outgroup B all.vcf.gz ind_pop.list momi2.gz. I got the result, but at the same time I got the error No BED provided, will need to specify length manually with mutation rate. Will there be any bad errors for the subsequent steps if I just use this result?

Thank you all.

jackkamm commented 1 year ago

It is just a warning, and there shouldn't be any errors.

If you want, you can instead specify the genome size by using the length parameter in DemographicModel.set_data.

Alternatively, momi2 can perform inference without knowing the genome size or mutation rate -- though it may affect power or identifiability, depending on the model parametrization.

XiaXiaTianTian commented 1 year ago

I tried. Thank you so much.