PEDANT: a program for estimating error rates in microsatellite genotype data. v1.0 (26 January 2007)

Introduction

Pedant is a program for estimating maximum likelihood allelic dropout and false allele error rates from duplicate microsatellite genotypes in the absence of reference genotypes. The code is written in Delphi 7.0 (which is based on Turbo Pascal).The main function of Pedant is to estimate error rates with confidence intervals from real genotypic data. In addition, Pedant can perform simulations, allowing you to decide how many samples you need to replicate to give a desired level of accuracy to your error rate estimates. Box A of the poster explains why it's useful to estimate dropout and false allele error rates separately.If you download Pedant, please let me know by email at pcdjohnson [at] gmail [dot] com.References

• Johnson PCD, Haydon DT (2007). Maximum likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data. Genetics 175 (2), 827-842.

• Johnson PCD, Haydon DT (2007). Software for quantifying and simulating microsatellite genotyping error. Bioinformatics and Biology Insights 1, 71-75.

Platforms

Pedant (pedant.exe) works on all versions of Windows going back at least as far as Windows 98. It may also work on older versions.

Installation

• 1. Create a folder from which to run the program (e.g. C:\Program Files\Pedant).

  2. Download the file pedant.zip unzip the files (executable, instructions, pdf poster and sample data file) into the folder.

What's new in Pedant 1.0 from version beta 1.3

• • The simulations now allow you to explore the effect of deviation from Hardy-Weinberg equilibrium by varying the inbreeding coefficient, FIS.

  • Update 8th January 2007: file conversion from Genepop to Pedant. Ideally Pedant would accept input files in some widely used format like Genepop. As I don't have time to do that at the moment, I've written a conversion program as an R script (pedant_converter.R), which is included in pedant.zip. Further instructions are written in the R script.

  • Bug fix 5th September 2007: Pedant Converter generated a warning with the latest version of R (v2.5.1).