Suggestions for dealing with batch effects

[davidecarlson]

Suggestions for dealing with batch effects

[fgvieira]

Hi Dave,

are all these samples from the same population? ngsF infers inbreeding by looking at deviations from HWE, so the analysis should be done per population.

That said, I have actually seen this before, where heterogeneous coverage can lead to some bias in the estimates.
To be sur

Since you have ok good coverage, the easiest would be to downsample high coverage samples to ~5-10x. This coverage should be enough to estimate F.

[davidecarlson]

Thanks for your response, and sorry for not following up earlier. It's a little bit hard to define what a population is in this system, but the samples should probably not be considered to be from the same population. I'll try your suggestions, thanks!