PedCut protocols

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PedCut specifications


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
PEDIG, PedHunter
Source code URL
Maintained Yes


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  • person_outline Yurii S. Aulchenko <>

Publication for PedCut

PedCut in pipelines

PMCID: 5916965
PMID: 29725345
DOI: 10.3389/fgene.2018.00133

[…] 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 […]

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

[…] when disease snps with recessive, additive, and dominant modes of inheritance and odds ratios of 1.1, 1.5, 2.0, and 5.0 were simulated. we generated subpedigrees with a maximum bit-size of 24 using pedcut and performed two-point and multipoint linkage using merlin. we also ran mqls on the subpedigrees and unified pedigree. we saw no inflation of type 1 error when running mqls on either […]

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PedCut in publications

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

[…] 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 […]

PMCID: 4144469
PMID: 25519312
DOI: 10.1186/1753-6561-8-S1-S109

[…] 3 for 959 individuals from 20 original pedigrees; of these individuals, 344 had hypertension and 506 did not. as a result of the limitations of our computing facility for linkage analysis, pedcut [] was used to split large pedigrees with members greater than 20 bits into smaller pedigrees to enable analyses by merlin []. consequently, we analyzed a total of 138 pedigrees with 1495 […]

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

[…] 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 […]

PMCID: 3633859
PMID: 23626830
DOI: 10.1371/journal.pone.0062545

[…] relationships after merging in only two generations from the complete pedigree, i.e., by merging in the parents and grandparents of all study subjects, and trimming the resulting pedigrees using pedcut with a maximum bit size of 100. to assess the impact of pedigree complexity on power, we repeated simulations using the complete 13-generation pedigree., note – pedigree trimming yielded 177 […]

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

[…] with missing test scores due to technical problems., 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 […]

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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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