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
ANGSD can estimate the 'F' on a single site basis. For method details see here, this can be be used for an HWE test. This is done by using:
- -HWE_pval
By choosing HWE_pval 1, no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in .hwe.gz file.
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.
Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating per individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output
- NB If in doubt if a specific analysis will work with inbreeding send an email.
HWE and Inbreeding estimates
And the most recent version of the stand alone program is here .