GVCHAP: A Computing Pipeline for Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers.

ABSTRACT: Haplotype prediction models open many possibilities to improve the accuracy of genomic selection but require more data processing and computing time than single-SNP prediction models. To facilitate haplotype analysis for genomic prediction and estimation using structural and functional genomic information, we developed a computing pipeline to implement haplotype analysis with capabilities for preparation of input data for haplotype analysis, genomic prediction and estimation using GVCHAP, and analysis of GVCHAP results. Data preparation includes utility programs for haplotype imputing; defining haplotype blocks by a fixed number of SNPs, a fixed distance in base pairs per block, or user defined block lengths based on structural or functional genomic information or a mixture of both types o

SUBMITTER: Prakapenka D 

PROVIDER: S-EPMC7154123 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature