GVCHAP: A Computer Package for Genomic Prediction and Estimation Using Haplotypes and Single SNPs

The GVCHAP computer package is designed to integrate haplotype and single-SNP analysis for genomic prediction and estimation. This package currently has three shared-memory parallel computing programs: GVCHAP for genomic prediction and variance component estimation, GCORRMA for calculating genomic relationships for multi-allelic markers such as microsatellite markers or haplotypes where each haplotype is treated as an allele, and HAPBLOCK for defining haplotype blocks and haplotypes within each block. GVCHAP calculates GBLUP, reliability of GBLUP, additive and dominance variance components, heritability of each haplotype block (or a multi-allelic marker) and heritability of each SNP, and total hertitability of haplotype blocks and single SNPs. The user has the option to use haplotypes only, single-SNPs only, or haplotypes and single-SNPs jointly; or additive effects only, dominance effects only, or additive and dominance effects jointly. GCORRMA calculates additive and dominance relationship matrices for multi-allelic markers or haplotypes treated as multiple alleles. HAPBLOCK defines haplotype blocks according to user specified boundaries of each block and defines haplotypes within each haplotype block. These results are used as an input file for GVCHAP and GCORRMA. Defining haplotype blocks and haplotypes otherwise is an extremely labor intensive process. HAPBLOCK reduces this labor intensive process to an automatic process and greatly improves the efficiency of haplotype analysis for genomic prediction and estimation.