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

Dzianis Prakapenka, Chunkao Wang, Zuoxiang Liang, Cheng Bian, Cheng Tan, Yang Da

Research output: Contribution to journalArticlepeer-review


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 of information; and defining haplotype genotypes within each haplotype block. GVCHAP is the main program for genomic prediction and estimation, calculates GREML (genomic restricted maximum likelihood) estimates of variance components and heritabilities, and calculates GBLUP (genomic best linear unbiased prediction) for additive and dominance values of single SNPs as well as additive values of haplotypes with reliability estimates for training and validation populations. A two-step strategy and a method of multi-node processing are implemented to remove the computing bottleneck due to the creation of genomic relationship matrices for large samples. The analysis of GVCHAP results includes calculation of observed prediction accuracies from validation studies and preparation of input files for graphical visualization of heritability estimates of haplotype blocks as well as estimates of SNP effects and heritabilities. The entire pipeline provides an efficient and versatile computing tool for identifying the most accurate haplotype model among many candidate haplotype models utilizing structural and functional genomic information for genomic selection.

Original languageEnglish (US)
Article number282
JournalFrontiers in Genetics
StatePublished - Apr 7 2020

Bibliographical note

Funding Information:
The Minnesota Supercomputer Institute at the University of Minnesota provided supercomputer computing time and storage for this research. Funding. This research was supported by grant no. 2018-67015-28128 from the USDA National Institute of Food and Agriculture, and by project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© Copyright © 2020 Prakapenka, Wang, Liang, Bian, Tan and Da.


  • genomic selection
  • haplotype
  • heritability
  • prediction accuracy
  • SNP

PubMed: MeSH publication types

  • Journal Article

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