ped_draw: pedigree drawing with ease
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SOFTWARE
ped_draw: pedigree drawing with ease Matt Velinder* , Dillon Lee and Gabor Marth *Correspondence: [email protected] Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
Abstract Background: Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples. While the text based format of ped files is efficient for computational methods, it is not immediately intuitive to a bioinformatician or geneticist trying to understand family structures, many of which encode the affected status of individuals across multiple generations. The visualization of pedigrees into connected nodes with descriptive shapes and shading provides a far more interpretable format to recognize visual patterns and intuit family structures. Despite these advantages of a visual pedigree, it remains difficult to quickly and accurately visualize a pedigree given a pedigree text file. Results: Here we describe ped_draw a command line and web tool as a simple and easy solution to pedigree visualization. Ped_draw is capable of drawing complex multi-generational pedigrees and conforms to the accepted standards for depicting pedigrees visually. The command line tool can be used as a simple one liner command, utilizing graphviz to generate an image file. The web tool, https://peddraw.github.io, allows the user to either: paste a pedigree file, type to construct a pedigree file in the text box or upload a pedigree file. Users can save the generated image file in various formats. Conclusions: We believe ped_draw is a useful pedigree drawing tool that improves on current methods due to its ease of use and approachability. Ped_draw allows users with various levels of expertise to quickly and easily visualize pedigrees. Keywords: Pedigree, Genetics, Mendelian, Family, Family studies, Generation, Inheritance, Drawing, Ped, Visualization
Background Pedigree files are text files that convey important information about the samples within a genetics or bioinformatics study [4]. This includes, at a minimum, for each sample: a kindred/family identifier, a sample identifier, a paternal identifier, a maternal identifier, a sex identifier (1 = male, 2 = female), and an affected status or phenotype identifier (1 = unaffected, 2 = affected) [3]. This text encoding is efficient for computational tools, but is difficult for a human user to visually parse and understand family and inheritance relationships. As such, bioinformaticians and geneticists typically rely on visual depictions of pedigrees where each individual is a node in a connected network, with: squares representing males, circles representing females, unshaded nodes representing © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit t
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