GCTA-GREMLd: estimating dominance variance from GWAS data

--make-grm-d
or
--make-grm-d-bin
Estimate the dominance genetic relationship matrix (GRM) between pairs of individuals from a set of SNPs and save the lower triangle elements of the dominance GRM to binary files. eg. test.grm.d.bin, test.grm.d.N.bin, test.grm.d.id
Output file format:
test.grm.d.bin Binary file which contains the lower triangle elements of the dominance GRM).
test.grm.d.N.bin Binary file which contains the number of SNPs used to calculate the dominance GRM).
test.grm.d.id No header line; columns are family ID and individual ID

--make-grm-d-gz
Estimate the dominance GRM, save the lower triangle elements to a compressed text file (e.g. test.grm.d.gz) and save the IDs in a plain text file (e.g. test.grm.d.id).
Output format:
test.grm.d.gz (No header line; columns are indices of pairs of individuals (row numbers of the test.grm.d.id), number of non-missing SNPs and the estimate of dominance genetic relatedness)
1    1     1000       0.0021      
2    1      998        0.0231      
2    2      999        0.0238      
3    1     1000       0.0031      
.....

test.grm.d.id (no header line; columns are family ID and individual ID)
011    0101    
012    0102    
013    0103    
.....


Examples:

# Calculating the additive GRM from all the autosomal SNPs
gcta64 --bfile test --autosome --make-grm --thread-num 10 --out test_add

# Calculating the dominance GRM from all the autosomal SNPs
gcta64 --bfile test --autosome --make-grm-d --thread-num 10 --out test_domi

# Estimating additive and dominance genetic variance by fitting an AD model
gcta64 --reml --mgrm add_domi_grm.txt --pheno test.phen --thread-num 10 --out test_add_domi

# format of add_domi_grm.txt (no headline; each line represents the prefix of a GRM file)
test_add
test_domi

# Note that most of the other GCTA options (e.g. --extract and --keep) are also valid for these analyses


References:

Method paper: Zhu Z, Bakshi A, Vinkhuyzen AA, Hemani G, Lee SH, Nolte IM, van Vliet-Ostaptchouk JV, Snieder H, The LifeLines Cohort Study, Esko T, Milani L, Mägi R, Metspalu A, Hill WG, Weir BS, Goddard ME, Visscher PM, Yang J (2015) Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits. Am J Hum Genet, 96: 1-9. [PubMed ID: 25683123]

GCTA software: Yang J, Lee SH, Goddard ME and Visscher PM. GCTA: a tool for Genome-wide Complex Trait Analysis. Am J Hum Genet. 2011 Jan 88(1): 76-82. [PubMed ID: 21167468]