Compute SNP effect

HIBLUP now can compute the additive and dominant effects for all SNPs. There are two ways to compute SNP effects, the first way is to add flag --snp-effect in the command when fitting single trait, multiple traits model, or solving mixed model:

# compute additive SNP effect by SSGBLUP of single trait model
./hiblup --single-trait
         --pheno demo.phe
         --pheno-pos 8
         --bfile demo
         --pedigree demo.ped
         --add
         --snp-effect
         --thread 32
         --out demo

the second way is to derive SNP effect from prior calculated GEBVs:

# compute dominant SNP effect
./hiblup --snp-effect
         --gebv demo.gebv.d.txt
         --bfile demo
         --dom
         --thread 32
         --out demo

The file format of GEBVs can be found at here. The genotype file specified by --bfile is used to construct GRM and compute SNP effect, for the second way, HIBLUP will construct additive or dominant GRM for individuals, to save time, users can provide prior calculated GRM, HIBLUP will use it directly:

# compute additive and dominant SNP effect
./hiblup --snp-effect
         --gebv demo.gebv.ad.txt
         --bfile demo
         --xrm demo.GA,demo.GD
         --add --dom
         --thread 32
         --out demo

The SNP effects of all SNPs are stored in file demo.snpeff.

NOTE

If the GEBVs are calculated by using a weight GRM, please remember to provide the same weights of all SNPs to flag --snp-weight.