Allow for negative F

[fgvieira]

Allow for negative F (-1 < F < 1) to accommodate other deviations from HWE

[hemstrow]

Hey @fgvieira , we've recently been getting lots of 0 estimates with a few datasets. If this issue hasn't been implemented yet, does that mean you get 0s whenever you have a heterozygote excess with ngsF?

[partridc]

Hey @fgvieira , we've recently been getting lots of 0 estimates with a few datasets. If this issue hasn't been implemented yet, does that mean you get 0s whenever you have a heterozygote excess with ngsF?

I'm having the same issue. I'm using ngsF to calculate Fis for a low coverage ngs dataset. Whenever calculating individual Fis all of the values are 0. However, based on the locus-level Fis from angsd, I'm expecting high levels of heterozygote excess. Is there a specific setting to allow for negative F? Thanks!

[fgvieira]

Currently ngsF does not support negative inbreeding values and, as such, will report values of 0 if there is an excess of heterozygotes.
Unfortunately, I don't think I'll have the time to implement this feature but contributions are welcome! 😄