Similar protocols

Pipeline publication

[…] nongenotyped markers for the individuals genotyped at low density (). Imputation approaches have been successfully and widely applied in breeding programs for several livestock and crop species (e.g., ; ; ; ; ). The accuracy of imputation is affected by several factors, including population structure, the number of SNPs in the imputation panel, the level of relatedness between reference and test data, effective population size, the inherent accuracy of the method used for imputation, and the degree to which markers are correctly ordered along the genome map (e.g., ; ; ; ). The methods applied for genotype imputation can broadly be split into two categories: (i) population approaches such as Beagle (), MaCH () and IMPUTE2 (), which utilize linkage disequilibrium (LD) between markers, and (ii) pedigree-based approaches such as PHASEBOOK (), findhap (), and AlphaImpute (), which harness genetic relationships (pedigree) in addition to LD. The latter approaches are suitable for data originating from typical livestock and aquaculture breeding programs, where large numbers of pedigreed individuals with genotype and phenotype data are routinely available., While research into imputation methods and their application to breeding programs has been extensive for livestock and crop species, they have not yet been widely tested in aquaculture species (; ). In part, this is due to the previous lack of genomic resources (e.g., SNP genotyping arrays and reference genome sequences) for many aquaculture species (, ). In recent ye […]

Pipeline specifications

Software tools BEAGLE, IMPUTE, PHASEBOOK