Abstract
BackgroundPedigree 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.ResultsHere 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.ConclusionsWe 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.
Highlights
Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples
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
This accepted format allows for rapid and intuitive visualization of family structures and how affected status is segregating in the family
Summary
The input for ped_draw is a ped file and the output is an image file (generated by graphviz). Ped files can contain multiple distinct families/kindreds, as specified by the first column of the file This is interpreted by ped_draw and two distinct pedigrees are drawn (Fig. 1b). An extended four generation family with multiple affected children across multiple generations is drawn (Fig. 1d) In these examples and others, ped_draw draws the pedigree in the accepted “tree” representation, connecting all related nodes, assigning node shaped based on sex, labels nodes based on sample name and shades all affected nodes grey. This allows geneticists and bioinformaticians to readily visualize relatedness between samples and identify inheritance modes through multiple generations. Numerous other examples of pedigrees drawn by ped_draw, including pedigrees from the CEPH families, can be found on the Github repository under examples/
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