Ellen M. Wijsman: Software and data

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• New, released March 18 2013:
  GIGI: Genotype imputation for dense markers in (large) pedigrees. See: Cheung CYK, Thompson EA, Wijsman EM (2013) GIGI: An approach to effective imputation of dense genotypes on large pedigrees. American Journal of Human Genetics (in press).
• lnkg2lmlnk, released Mar. 12, 2012. A new converter from Linkage-style to Morgan ver 3 style data files with some example data files here.
• plotIBD, Released Nov. 18, 2011. A perl script to assist with plotting sampled inheritance vectors in pedigrees, as described in Marchani EE, Wijsman EM (2011) Estimation and visualization of identity-by-descent within pedigrees simplifies interpretation of complex trait analysis. Human Heredity 72(4):289-297.
• Relationship corrected chi-square testing and README file:. This release (Apr. 2, 2010) replaces the version of the kinship estimation program and ancillary programs released Nov. 12, 2009.
• Kinship and README file: Released Nov. 12, 2009. Software to carry out computations to estimate kinship coefficients for case-control analyses in the presence of cryptic relatedness, as described in the paper: Choi et al (2009) "Case-control association testing in the presence of unknown relationships" Genetic Epidemiology (2009), 35:668-678, PMID: 19333967
• PANGAEA for the MORGAN package or Loki
• lnkg2lmm. Released Sept. 1, 2007. A Perl script to convert linkage-style files to MORGAN-lm_markers-style files, also distributed from the PANGAEA/MORGAN distribution site.
  Two sets of example files include a binary trait, and a quantitative trait , both based on a couple of simulated data sets from the paper by Wijsman et al (2006) AJHG 79:846-858.
• Loki: Perl scripts for Loki; and two versions of Loki: Loki ver. 2.4.5, Loki ver. 2.4.7. Perl scripts were released Sept. 1, 2007: additional useful scripts for manipulating files from Loki are provided as-is. These are scripts that members of my group have written and that carry out commonly-used tasks. These scripts include computation of Bayes Factors for linkage by uniform intervals or by inter-marker intervals (different from the L-score distributed with Loki); flipping of QTL models to eliminate the model bimodality that is intrinsic in the analysis approach; extracting QTL models that meet particular conditions; and extracting QTL models that fall in an ellipse in a heterozygote-homozygote effect scatter plot. See beginning of each perl script for program documentation. Note that the assumption behind these scripts is that you are using Loki ver 2.4.5, 2.4.6, or 2.4.7.
• SimSuite Ver. 1.0 Scripts, README file, and Examples: Released mar. 15, 2009. A suite of Perl scripts to manage trait simulation from Loki output files, marker simulation, and analysis of results with Loki and/or SOLAR, described by Igo & Wijsman (2008) Empirical significance values for linkage analysis: trait simulation using posterior model distributions from MCMC oligogenic segregation analysis. Genetic Epidemiology 32:119-131.
• Simulated data used in the paper by Wijsman et al (2006) AJHG 79:846-858 is available at the PANGAEA distribution site.
• Other programs are currently distributed informally, and in a state that is "as is". Contact me if you are interested.