Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation

John Hickey; Brian Kinghorn; Bruce Tier; Julius H Van Der Werf

Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation

John Hickey
, Brian Kinghorn
, Bruce Tier
, Julius H Van Der Werf

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

A Long Range Haplotype Imputation algorithm was developed and combined with a Recursive Long Range Phasing algorithm. These were tested on simulated SNP data sets which had structures possibly similar to those found in sheep and dairy cattle. Performance, measured by accuracy of phasing (>97.6%) and computing time, was competitive in comparison to industry standard software.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	A Safari, B Pattie, B Restall
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	72-75
Volume	18
ISBN (Print)	0646521039, 9780646521039
Publication status	Published - 2009
Event	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics - Barossa Valley, Australia Duration: 27 Sept 2009 → 2 Oct 2009

Conference

Conference	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Barossa Valley, Australia
Period	27/09/09 → 2/10/09

Keywords

Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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https://hdl.handle.net/1959.11/5117

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Hickey, J., Kinghorn, B., Tier, B., & Van Der Werf, J. H. (2009). Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation. In A. Safari, B. Pattie, & B. Restall (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 18, pp. 72-75). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/5117

Hickey, John ; Kinghorn, Brian ; Tier, Bruce et al. / Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / A Safari ; B Pattie ; B Restall. Vol. 18 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. pp. 72-75

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title = "Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation",

abstract = "A Long Range Haplotype Imputation algorithm was developed and combined with a Recursive Long Range Phasing algorithm. These were tested on simulated SNP data sets which had structures possibly similar to those found in sheep and dairy cattle. Performance, measured by accuracy of phasing (>97.6\%) and computing time, was competitive in comparison to industry standard software.",

keywords = "Quantitative Genetics (incl Disease and Trait Mapping Genetics)",

author = "John Hickey and Brian Kinghorn and Bruce Tier and \{Van Der Werf\}, \{Julius H\}",

year = "2009",

language = "English",

isbn = "0646521039",

volume = "18",

pages = "72--75",

editor = "A Safari and B Pattie and B Restall",

booktitle = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

note = "AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 27-09-2009 Through 02-10-2009",

}

Hickey, J, Kinghorn, B, Tier, B & Van Der Werf, JH 2009, Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation. in A Safari, B Pattie & B Restall (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 18, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 72-75, AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 27/09/09. <https://hdl.handle.net/1959.11/5117>

Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation. / Hickey, John; Kinghorn, Brian; Tier, Bruce et al.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / A Safari; B Pattie; B Restall. Vol. 18 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. p. 72-75.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation

AU - Hickey, John

AU - Kinghorn, Brian

AU - Tier, Bruce

AU - Van Der Werf, Julius H

PY - 2009

Y1 - 2009

N2 - A Long Range Haplotype Imputation algorithm was developed and combined with a Recursive Long Range Phasing algorithm. These were tested on simulated SNP data sets which had structures possibly similar to those found in sheep and dairy cattle. Performance, measured by accuracy of phasing (>97.6%) and computing time, was competitive in comparison to industry standard software.

AB - A Long Range Haplotype Imputation algorithm was developed and combined with a Recursive Long Range Phasing algorithm. These were tested on simulated SNP data sets which had structures possibly similar to those found in sheep and dairy cattle. Performance, measured by accuracy of phasing (>97.6%) and computing time, was competitive in comparison to industry standard software.

KW - Quantitative Genetics (incl Disease and Trait Mapping Genetics)

UR - http://www.aaabg.org/proceedings18/files/hickey072.pdf

UR - http://trove.nla.gov.au/work/36420775

M3 - Conference contribution

SN - 0646521039

SN - 9780646521039

VL - 18

SP - 72

EP - 75

BT - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

A2 - Safari, A

A2 - Pattie, B

A2 - Restall, B

PB - Association for the Advancement of Animal Breeding and Genetics (AAABG)

CY - Armidale, Australia

T2 - AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics

Y2 - 27 September 2009 through 2 October 2009

ER -

Hickey J, Kinghorn B, Tier B, Van Der Werf JH. Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation. In Safari A, Pattie B, Restall B, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 18. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2009. p. 72-75

Phasing of SNP Data by Combined Recursive Long Range Phasing and Long Range Haplotype Imputation

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