Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees

Andrew Whalen; Roger Ros Freixedes; David L. Wilson; Gregor Gorjanc; John Hickey

doi:10.1186/s12711-018-0438-2

Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees

Andrew Whalen
, Roger Ros Freixedes
, David L. Wilson
, Gregor Gorjanc
, John Hickey

Royal (Dick) School of Veterinary Studies

Research output: Contribution to journal › Article › peer-review

Abstract

In this paper, we extend multi-locus iterative peeling to provide a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, called hybrid peeling, uses multi-locus iterative peeling to estimate shared chromosome segments between parents and their offspring at a subset of loci, and then uses single-locus iterative peeling to aggregate genomic information across multiple generations at the remaining loci.

Original language	English
Article number	67
Number of pages	15
Journal	Genetics Selection Evolution
Volume	50
Issue number	1
DOIs	https://doi.org/10.1186/s12711-018-0438-2
Publication status	Published - 18 Dec 2018

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10.1186/s12711-018-0438-2

Hybrid peeling for fast and accurate
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Analysis of quantitative genetic traits in a huge data set
Hickey, J. (Principal Investigator) & Hill, D. (Co-investigator)
Biotechnology and Biological Sciences Research Council
1/05/16 → 30/04/19
Project: Research
Precision Breeding: Broilers from Sequence to Consequence
Hickey, J. (Principal Investigator) & Woolliams, J. (Co-investigator)
Biotechnology and Biological Sciences Research Council
1/11/15 → 31/10/18
Project: Research
Innovative NextGen pig breeding using DNA sequence data
Hickey, J. (Principal Investigator) & Woolliams, J. (Co-investigator)
Biotechnology and Biological Sciences Research Council
1/11/15 → 31/10/18
Project: Research

Cite this

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abstract = "In this paper, we extend multi-locus iterative peeling to provide a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, called hybrid peeling, uses multi-locus iterative peeling to estimate shared chromosome segments between parents and their offspring at a subset of loci, and then uses single-locus iterative peeling to aggregate genomic information across multiple generations at the remaining loci. ",

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AU - Hickey, John

PY - 2018/12/18

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Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees

Abstract

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Projects

Analysis of quantitative genetic traits in a huge data set

Precision Breeding: Broilers from Sequence to Consequence

Innovative NextGen pig breeding using DNA sequence data

Cite this