The homozygosity and heterozygosity are defined as the proportion of homozygous and heterozygous of an individual, it can be easily obtained from HIBLUP by using the flag --homo and --hete, respectively.
Homozygosity
./hiblup --bfile demo --homo --out demo
A file named demo.homo will be generated as following:
id a1a1 a2a2 IND0701 0.42255 0.201235 IND0702 0.415291 0.204923 IND0703 0.426455 0.199282
Heterozygosity
./hiblup --bfile demo --hete --out demo
A file named demo.hete will be generated as following:
id a1a2 IND0701 0.376216 IND0702 0.379786 IND0703 0.374263