Ellen M. Wijsman: Software and data

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New in January 2019: release of GIGI2, a faster and more efficient memory-using version of GIGI
New in June 2018: Release of ADMIXFRQ, GIGI-Quick
New in October 2017: Updated release of famSKAT-RC
New in August 2017: AFC (release August 1, 2017)
New in 2015: PBAP (release August 7, 2015), updated user manual, Aug. 24, 2015; New releases of GIGI (ver 1.06.1) and GIGI-Pick (ver 1.06); release of SharedHap

• GIGI2: a faster version of GIGI. Description of the algorithms: "Ullah et al 2019, GIGI2: A Fast Approach for Parallel Genotype Imputation in Large Pedigrees." bioRxiv, Source code for GIGI2, and the webserver version.
• ADMIXFRQ from github, or here software implementing the approach described in Nafikov et al (2018) Analysis of Pedigree Data in Populations with Multiple Ancestries: Strategies for Dealing with Admixture in Caribbean Hispanic Families from the ADSP. Genetic Epidemiology 42:500-515.
• GIGI-Quick described in Kunji K, Ullah E, Nato AQ Jr, Wijsman EM, Saad M (2018) "GIGI-Quick: A fast approach to impute missing genotypes in genome-wide association family data". Bioinformatics 34(9):1591-1593.
• famSKAT-RC New release (v1.03) of famSKAT-RC, described in Saad & Wijsman (2014) "Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees" Genetic Epidemiology, 38:579-590.
• AFC R code with examples, version 1.0, released August 1, 2017. These files replace the relationship corrected chi-square test listed below for use in the setting of a shared control sample, and add the WQLS and famSKAT tests in the same shared controls context. See: Saad M and Wijsman EM (2017) Association Score Testing for Rare Variants and Binary Traits in Family Data with Shared Controls, Briefings in Bioinformatics (published August 31 online).
• PBAP, Version 1.0 released August 7, 2015, with updated User Manual. See: Nato AQ Jr, Chapman NH, Sohi HK, Nguyen HD, Brkanac Z, Wijsman EM (2015) PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers. Bioinformatics 31(23):3790-3798).
• SharedHap Released Jan. 14, 2015. Software that implements the haplotype-sharing visualization approach described by Kim et al (2014) Visualization of haplotype sharing patterns in pedigree samples. Human Heredity 78:1-8.
• initial release of famSKAT-RC, Released July 25, 2014. R scripts, to carry out a combined rare- and common-variant gene-based test of association in the presence of related individuals, and Ped_Pop as tarred,gzipped file , or Ped_Pop as a zipped file, a C program for combining genotype imputation from GIGI and Beagle, or other pairs of genotype imputation approaches that are based on pedigree and population-based methods. For details of either method, see the paper: Saad and Wijsman (2014) "Combining family- and population-based imutation data for association analysis of rare and common variants in large pedigrees" Genetic Epidemiology, 38:579-590.
• GIGI-Check, Revision 1.06 released February 2, 2015. Detection of Mendelian consistent genotyping errors in dense SNP markers in pedigrees. See: Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2014) Detection of Mendelian Consistent Genotyping Errors in Pedigrees. Genetic Epidemiology 38(4):291-299. (ver. 1.0 Released Apr. 25, 2014).
• GIGI-Pick Revision 1.06 released February 2, 2015. Selection of ideal subjects in pedigrees to sequence. See: Cheung CYK, Blue EM, Wijsman EM (2014) A statistical choice to quide sequencing choices in pedigrees. American Journal of Human Genetics 94(2):257-267. (ver. 0.9 Released Apr. 25, 2014).
• GIGI: Revision 1.06.1 released January 31, 2015. 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 92:504-516. (ver. 1.06 released Jan. 14, 2015; ver 1.05 released Aug. 16, 2014; ver 1.04 released Nov. 15, 2013; ver 1.03 released July 19, 2013; ver 1.02 released Mar. 6, 2013)
• 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 as the "SIMULATED TEST DATA" on the PANGAEA distribution site.
• Other programs are currently distributed informally, and in a state that is "as is". Contact me if you are interested.