Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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, View ORCID ProfileGregor Gorjanc, John M Hickey
doi: https://doi.org/10.1101/228999
Andrew Whalen
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roger Ros-Freixedes
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David L Wilson
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gregor Gorjanc
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gregor Gorjanc
John M Hickey
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

In this paper we extend multi-locus iterative peeling to be 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, and then uses single-locus iterative peeling to aggregate genomic information across multiple generations. Using a synthetic dataset, we first analysed the performance of hybrid peeling for calling and phasing alleles in disconnected families, families which contained only a focal individual and its parents and grandparents. Second, we analysed the performance of hybrid peeling for calling and phasing alleles in the context of the full pedigree. Third, we analysed the performance of hybrid peeling for imputing whole genome sequence data to the remaining individuals in the population. We found that hybrid peeling substantially increase the number of genotypes that were called and phased by leveraging sequence information on related individuals. The calling rate and accuracy increased when the full pedigree was used compared to a reduced pedigree of just parents and grandparents. Finally, hybrid peeling accurately imputed whole genome sequence information to non-sequenced individuals. We believe that this algorithm will enable the generation of low cost and high accuracy whole genome sequence data in many pedigreed populations. We are making this algorithm available as a standalone program called AlphaPeel.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted December 04, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
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 M Hickey
bioRxiv 228999; doi: https://doi.org/10.1101/228999
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
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 M Hickey
bioRxiv 228999; doi: https://doi.org/10.1101/228999

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genetics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3477)
  • Biochemistry (7316)
  • Bioengineering (5293)
  • Bioinformatics (20188)
  • Biophysics (9972)
  • Cancer Biology (7697)
  • Cell Biology (11243)
  • Clinical Trials (138)
  • Developmental Biology (6415)
  • Ecology (9911)
  • Epidemiology (2065)
  • Evolutionary Biology (13270)
  • Genetics (9347)
  • Genomics (12543)
  • Immunology (7667)
  • Microbiology (18928)
  • Molecular Biology (7415)
  • Neuroscience (40866)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2124)
  • Physiology (3137)
  • Plant Biology (6836)
  • Scientific Communication and Education (1268)
  • Synthetic Biology (1890)
  • Systems Biology (5295)
  • Zoology (1083)