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 please email and ask.
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.