PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

Roeland E. Voorrips; Marco C.A.M. Bink; Johannes W. Kruisselbrink; Herma J.J. Koehorst-van Putten; Eric van de Weg

doi:10.1007/s11032-016-0539-y

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

Roeland E. Voorrips^*, Marco C.A.M. Bink, Johannes W. Kruisselbrink, Herma J.J. Koehorst-van Putten, Eric van de Weg

^*Corresponding author for this work

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

46 Citations (Scopus)

Abstract

In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called “haploblocks”. Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.

Original language	English
Article number	119
Journal	Molecular Breeding
Volume	36
DOIs	https://doi.org/10.1007/s11032-016-0539-y
Publication status	Published - 2016

Keywords

Haploblock
Haplotyping
Pedigree
SNP

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title = "PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees",

abstract = "In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called “haploblocks”. Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.",

keywords = "Haploblock, Haplotyping, Pedigree, SNP",

author = "Voorrips, {Roeland E.} and Bink, {Marco C.A.M.} and Kruisselbrink, {Johannes W.} and {Koehorst-van Putten}, {Herma J.J.} and {van de Weg}, Eric",

year = "2016",

doi = "10.1007/s11032-016-0539-y",

language = "English",

volume = "36",

journal = "Molecular Breeding",

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T2 - software for consistent assignment of marker haplotypes in pedigrees

AU - Voorrips, Roeland E.

AU - Bink, Marco C.A.M.

AU - Kruisselbrink, Johannes W.

AU - Koehorst-van Putten, Herma J.J.

AU - van de Weg, Eric

PY - 2016

Y1 - 2016

N2 - In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called “haploblocks”. Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.

AB - In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called “haploblocks”. Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.

KW - Haploblock

KW - Haplotyping

KW - Pedigree

KW - SNP

U2 - 10.1007/s11032-016-0539-y

DO - 10.1007/s11032-016-0539-y

M3 - Article

AN - SCOPUS:84981278125

SN - 1380-3743

VL - 36

JO - Molecular Breeding

JF - Molecular Breeding

M1 - 119

ER -

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

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Keywords

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