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.

Global estimate

This is simply the SFS Estimation for single samples. A short example is:

./angsd -i my.bam -anc ancestral.fa -dosaf 1 -gl 1
#OR
./angsd -i my.bam -anc ref.fa -dosaf 1 -fold 1
#followed by the actual estimation
./realSFS angsdput.saf.idx >est.ml

The heterozygosity is then:

#in R
a<-scan("est.ml")
a[2]/sum(a)