ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
HWE and Inbreeding estimates
Filipe G. Vieira has been extending the ANGSD feature set by
- A method for estimating inbreeding (deviation from Hardy-Weinberg) based on output from ANGSD.
- Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.
- NB If in doubt if a specific analysis will work with inbreeding send an email.
HWE and Inbreeding estimates
For method details see here And the most recent version of the stand alone program is here https://github.com/fgvieira/ngsF.