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Protocols

PedCut specifications

Information


Unique identifier OMICS_13150
Name PedCut
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.19
Stability Stable
Requirements
PEDIG, PedHunter
Source code URL http://mga.bionet.nsc.ru/soft/pedcut/pedcut_1.19.tar.gz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Yurii S. Aulchenko

Publication for PedCut

PedCut citations

 (7)
call_split

A Genome Wide Linkage Study for Chronic Obstructive Pulmonary Disease in a Dutch Genetic Isolate Identifies Novel Rare Candidate Variants

2018
Front Genet
PMCID: 5916965
PMID: 29725345
DOI: 10.3389/fgene.2018.00133
call_split See protocol

[…] ERF were used. The cases were linked in a single large pedigree of 23 generations. However, due to the linkage software restraints, the cases were clustered into 27 smaller (≤24 bits) families using PEDCUT software (). We used HaploPainter () to illustrate all 27 pedigrees (Supplementary Figure ). We then performed affected-only parametric linkage analysis in MERLIN software () using incomplete p […]

library_books

Determinants of retinal microvascular features and their relationships in two European populations

2017
PMCID: 5491231
PMID: 28509723
DOI: 10.1097/HJH.0000000000001408

[…] fter removing uninformative individuals, the pedigrees were still too large for analysis; therefore, they were trimmed to smaller informative pedigrees with a maximum bitsize of 50 using the software PedCut []. In the current analysis, pairs of closely related individuals with genotypes and retinal traits comprised 327 parent–child, 286 full sibs, 13 half-sibs, 492 first-degree cousins, 255 avuncu […]

call_split

Multipoint association mapping for longitudinal family data: an application to hypertension phenotypes

2016
BMC Proc
PMCID: 5133529
PMID: 27980655
DOI: 10.1186/s12919-016-0049-2
call_split See protocol

[…] ] out of 402 offspring on average) for phenotype (IV) “Longitudinal” (Table ). To compare phenotypes (I) and (II), only individuals with at least 2 measurements were included in the “ever” phenotype. PedCut [] was used to split large pedigrees with members more than 20 members into nuclear pedigrees. Consequently, we analyzed a total of 138 pedigrees with 1,495 individuals (the IDs for missing par […]

library_books

Evaluating Power and Type 1 Error in Large Pedigree Analyses of Binary Traits

2013
PLoS One
PMCID: 3643945
PMID: 23658753
DOI: 10.1371/journal.pone.0062615

[…] simpler pedigrees. Therefore, it is necessary to split the pedigree into smaller sub-pedigrees when performing linkage analysis on a data set exceeding these limitations. One method for doing this is PedCut , which generates sub-pedigrees with the maximal number of subjects of interest within a specified bit-size (two times the number of non-founders minus the number of founders ) limit conducive […]

library_books

Insulin resistance and metabolic syndrome are related to executive function in women in a large family based study

2010
PMCID: 2921069
PMID: 20585974
DOI: 10.1007/s10654-010-9476-y

[…] One large pedigree was extracted from the genealogical database, which was cut into smaller pedigrees before analyses with the software PedCut []. In total, 1,898 people with complete data could be linked to pedigrees with a maximum bit size of 18 and these were included in the analyses.Baseline descriptive analyses were performed wit […]

library_books

Genetic risk profiles for depression and anxiety in adult and elderly cohorts

2010
Mol Psychiatry
PMCID: 3142964
PMID: 20567237
DOI: 10.1038/mp.2010.65

[…] onio, TX, USA) using the ‘polygenic' option to adjust for pedigree kinship. Among 1886 people both genotyped and phenotyped, 1697 were clustered into pedigrees (using the pedigree splitting algorithm PedCut) and included in the family-based analysis. The remaining persons were not included in the analysis because they were also (distantly) related. The difference of the explained variance in the n […]


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PedCut institution(s)
Department of Epidemiology & Biostatistics, Genetic Epidemiology unit, Erasmus MC, Rotterdam, Netherlands; Siberian Division, Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia
PedCut funding source(s)
This work was supported by Netherlands Organization for Scientific Research (NWO, 91203014), the joint grant from the Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR), the Centre of Medical Systems Biology (CMSB), Hersenstichting Nederland, Internationale Stichting Alzheimer Onderzoek (ISAO), Alzheimer Association project number 04516, Hersenstichting Nederland project number 12F04(2).76, Interuniversity Attraction Poles (IUAP) program.

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