Calculate inbreeding and relationship coefficient

Inbreeding and relationship coefficients are derived from either pedigree or genotype information, HIBLUP firstly constructs additive numerator matrix, then derive and output the coefficients in file. The flag for inbreeding coefficient and relationship coefficient is --ibc and --rc, respectively.

Inbreeding coefficients

# derived from pedigree
./hiblup --ibc --pedigree demo.ped --thread 32 --out demo
# or derived from prior calculated PA matrix
./hiblup --ibc --xrm demo.PA --out demo

# derived from genotype
./hiblup --ibc --bfile demo --thread 32 --out demo
# or derived from prior calculated GA matrix
./hiblup --ibc --xrm demo.GA --out demo

The inbreeding coefficients are saved in file demo.ibc:

id        ibc
IND0702  0.00290048
IND0703  0.00262272
IND0704  0.00262272

Relationship coefficients

# derived from pedigree
./hiblup --rc --pedigree demo.ped --thread 32 --out demo
# or derived from prior calculated PA matrix
./hiblup --rc --xrm demo.PA --out demo

# derived from genotype
./hiblup --rc --bfile demo --thread 32 --out demo
# or derived from prior calculated GA matrix
./hiblup --rc --xrm demo.GA --out demo

The relationship coefficients are saved in file demo.rc:

id1     id2     rc
IND0701 IND0701 1
IND0701 IND0702 0.472652
IND0701 IND0703 0.0721178
IND0701 IND0704 0.0721178

1. The inbreeding coefficients and relationship coefficients can be calculated at a time, like:

./hiblup --ibc --rc --pedigree demo.ped --out demo
./hiblup --ibc --rc --bfile demo --out demo

2. The genomic inbreeding coefficients and relationship coefficients can be calculated by different methods using the flag --code-method, more details can be seen here.

./hiblup --ibc --rc --bfile demo --code-method 1 --out demo