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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
--ibc and
--rc
--rc, respectively.

Inbreeding coefficients

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# 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
# 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
# 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
demo.ibc:

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id ibc
IND0702 0.00290048
IND0703 0.00262272
IND0704 0.00262272
id ibc IND0702 0.00290048 IND0703 0.00262272 IND0704 0.00262272
id        ibc
IND0702  0.00290048
IND0703  0.00262272
IND0704  0.00262272

Relationship coefficients

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# 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
# 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
# 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
demo.rc:

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

NOTE

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

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./hiblup --ibc --rc --pedigree demo.ped --out demo
./hiblup --ibc --rc --bfile demo --out demo
./hiblup --ibc --rc --pedigree demo.ped --out demo ./hiblup --ibc --rc --bfile demo --out demo
./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
--code-method, more details can be seen here.

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