HWE and Inbreeding estimates
Site estimate of inbreeding coefficient (HWE test)
By choosing HWE_pval_F 1, no sites will be filtered but the p-value along with the frequency, and F for the sites will be dumped in .hweF.gz file.
Estimation of individual inbreeding coefficients
Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output