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ERROR CHECKING PROGRAMS

CHECKHET
*Description A program to detect genetically abnormal subjects in a case-control sample based on genotypes at multiple marker loci.
Authors Dave Curtis
References Curtis D, North BV, Gurling H, Blaveri E, Sham PC. (2002). A quick and simple method for detecting subjects with abnormal genetic background in case-control samples. Annals of Human Genetics, 66:235-244.
Website http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

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GENOCHECK
*Description GenoCheck is a program designed to identify genotypes that are likely to be errors. The statistical method was designed to identify typing error rather than pedigree errors, but is general enough to pinpoint any unlikely genotype still consistent with Mendelian inheritance.
Authors Dr. Meg Gelder Ehm(Glaxo Wellcome Inc.), Marek Kimmel, Robert W. Cottingham, Alejandro Schaffer, Ramana Idury, Shriram Krishnamurthi, Sandeep Gupta, G. Mark Lathrop.
References
  • Ehm MG, Cottingham RW Jr., Kimmel M. (1995). Error Detection in Genetic Linkage Data Using Likelihood Based Methods. Journal of Biological Systems, 3(1), 13-25.
  • Ehm MG, Kimmel M, Cottingham RW Jr. (1996). Error detection for genetic data, using likelihood methods. Am J Hum Genet, 58(1), 225-34.
Website http://softlib.rice.edu/geno.html

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GRR
*Description GRR is a Windows-based application for detecting pedigree errors via graphically inspecting the distribution for marker allele sharing among pairs of family members or all pairs of individuals in a study.
Authors Gonçalo Abecasis, S S Cherny, W O C Cookson, and L R Cardon
References Abecasis GR, Cherny SS, Cookson WOC, Cardon LR. (2001) GRR: graphical representation of relationship errors. Bioinformatics, 17(8), 742-743.
Website http://www.sph.umich.edu/csg/abecasis/GRR/

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PEDCHECK
*Description Identifying all Mendelian inconsistencies in pedigree data.
Authors J. R. O'Connell
References
  • O’Connell JR, Weeks DE. (1997). PedCheck: a program for identifying marker typing incompatibilities in linkage analysis. Am J Hum Genet, Suppl 60, A288.
  • O'Connell JR, Weeks DE. (1998). PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet, 63, 259-266.
Website http://watson.hgen.pitt.edu/register/docs/pedcheck.html

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PREST (Pedigree RElationship Statistical Test)
*Description Pedigree RElationship Statistical Test. PREST is a program that detects pedigree errors in general outbred pedigrees by use of genome-screen data. When a potential pedigree error is detected, our companion program, ALTERTEST, determines which relationships are compatible with the observed genotype data. Both programs are freely available on the web.
Authors Lei Sun, Kenneth Wilder, Mary Sara McPeek (Univ Chicago)
References McPeek M, Sun L. (2000). Statistical tests for detection of misspecified relationships by use of genome-screen data. American Journal of Human Genetics, 66, 1076-1094.
Website http://galton.uchicago.edu/~mcpeek/software/prest/

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RELCHECK
*Description Program for verifying the relationships between all pairs of individuals in a linkage study, by use of (autosomal) genome scan data, with allowance for the presence of genotyping errors.
Authors Karl W. Broman (Johns Hopkins Univ)
References
  • Boehnke M, Cox NJ. (1997). Accurate inference of relationships in sib-pair linkage studies. Am J Hum Genet, 61, 423-429.
  • Broman KW, Weber JL. (1998). Estimation of pairwise relationships in the presence of genotyping errors. Am J Hum Genet, 63, 1563-1564.
Website http://www.biostat.wisc.edu/~kbroman/software/

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SIBERROR (SibError)
*Description SibError is an algorithm that identifies pedigree errors in sibship data. Examples include half siblings, unrelated individuals, identical twins, and parental exclusions. The test statistic is based on the summation of the number of alleles shared by a pair of relatives for a large number of markers and the number of alleles and allele frequencies for those markers.
Authors Meg Gelder Ehm, Michael Wagner (Glaxo Wellcome, Inc.)
References Ehm M, Wagner M. (1998). Test statistic to detect errors in sib-pair relationship. Am J Hum Genet, 62, 181-188.

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* Description retrieved from http://linkage.rockefeller.edu/soft/