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.
Heterozygosity
The heterozygosity is the proportion of heterozygous genotypes.
This can either be a global estimate or a local estimate.
For diploid single samples the hetereo zygosity is simply second value in the SFS/AFS. An important aspect with this approach is that we DO NOT require to fix the major and minor. By fixing the ancestral we loop over the 3 possible derived alleles, or we can use the reference as the ancestral and fold the spectrum.