hsphase protocols

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hsphase specifications


Unique identifier OMICS_13145
Name hsphase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Hsphase requires a map file (name, chromosome and map positions), a genotype data file (numerically coded as 0, 1, 2 for the three genotypes and 9 for missing data) and a pedigree file (individuals and paternal ancestor).
Input format SNP
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Snowfall, RcppArmadillo
Maintained Yes



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  • person_outline Mohammad Ferdosi <>

Publications for hsphase

hsphase in pipelines

PMCID: 5859378
PMID: 29593780
DOI: 10.3389/fgene.2018.00082

[…] crosses performed in this experiment, the family structure of the offspring was unknown at the time of sampling. parentage assignment was performed using the rad-seq-derived snp data and the r/hsphase () software allowing for a maximum overall genotyping error of 4%. the pedigree obtained was further validated for possible erroneous assignments using fimpute ()., linkage map construction […]

PMCID: 4558911
PMID: 26337592
DOI: 10.1186/s12711-015-0148-y

[…] follows: minimum stack depth (m) = 30; distance between stacks (m) = 2; distance between catalog loci (n) = 1., parentage assignment was performed with vitassign v8-5.1 [] using 200 snps and with r/hsphase using all discovered snps and allowing for a maximum genotyping error of 3 % []. r v.3.0.1 was used for chi-square tests to detect significant deviations from the equal sex ratio […]

hsphase in publications

PMCID: 5043651
PMID: 27687320
DOI: 10.1186/s12711-016-0253-6

[…] 50k genotype data for a population of brahman cattle to analyze three traits: scrotal circumference (sc), age at puberty (agecl) and weight at first corpus luteum (wtcl). haplotypes were phased with hsphase and imputed with beagle. the relationship matrices were built using three methods based on haplotypes of different lengths. the log-likelihood was considered to define the optimum haplotype […]

PMCID: 5015933
PMID: 27402363
DOI: 10.1534/g3.116.032409

[…] cows (n=106), which were initially genotyped with a 50k snp chip, where the complete data set was described by . the sire was phased based on the daughter genotypes using the r package hsphase (). for convenience, only p=903 snps at which the sire was heterozygous were selected from bta1. the snp alleles were recoded corresponding to the sire haplotypes aa/bb. the paternal […]

PMCID: 4558911
PMID: 26337592
DOI: 10.1186/s12711-015-0148-y

[…] and 87 males) were assigned to a unique parental pair using vitassign [], by allowing a maximum of five mismatches in a test panel of 200 snps. resulting parentage assignments were confirmed with r/hsphase [], allowing for a maximum genotypic error of 3 %. sire 1 had the smallest number of progeny, while sire 4 had the largest number, for both dams. a correlation of 0.96 was found […]

PMCID: 4536601
PMID: 26272623
DOI: 10.1186/s12711-015-0142-4

[…] ovine snp50 beadchip. among the 53 862 single nucleotide polymorphisms (snps) on this array, 48 640 were used to perform a gwas using a linear mixed model approach. genotypes were phased with hsphase; to estimate snp haplotype effects, linkage disequilibrium blocks were identified in the detected qtl region., thirty-nine snps were associated with bw at a bonferroni-corrected genome-wide […]

hsphase institution(s)
The Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia; Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang, Korea
hsphase funding source(s)
This work was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ008196), Rural Development Administration, Republic of Korea and by an Australian Research Council Discovery Project DP130100542.

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