Relatedness, as a measure of shared genes, ranges from 0.0 (no relation) to 1.0 (exact clones). By considering all pairwise relatedness among a set of individuals an approximate pedigree, or family tree, can be built. In the past, such a pedigree chart was built manually by a compiling expert biologist. relped automates building such a pedigree, while allowing the expert biologist to overrule automated inference based on known relationships, parentage, and/or demographics.
Before using relped there are a few programs you need to install:
- Git: allows you to download
relped - Go: allows you to compile
relped - Graphviz: allows you to render
relped's output
After installing the programs above, getting relped installed should be as easy as:
go get -u github.com/rhagenson/relpedrelped has one required input, Relatedness, and two optional inputs, Parentage and Demographics.
Example:
ID1,ID2,Rel
123,456,0.50
...
Note that your columns must be named ID1,ID2, and Rel. If your file has duplicate entries of the same ID pair in either order, only the last entry will be used. Rel entries may be either a decimal value or one of: PO, FS, HS, U, indicating known parent-offspring, full-sibling, half-sibling, or unrelated pair, respectively.
Example:
ID,Sire,Dam
123,456,789
...
Note that your columns must be named ID,Sire, and Dam. If your file contains duplicate ID entries, only the last entry will be used.
Sire and Dam are used the same as if you had added a PO called record into the relatedness input between ID and either Sire or Dam with the additional information of known direction such that Sire and Dam are plotted above ID in the pedigree. Unknown Sire and/or Dam may be denoted via a 0 or ? entry.
Example:
ID,Sex,BirthYear
123,Male,1990
...
Note that your columns must be named ID,Sex, and BirthYear. If your file contains duplicate ID entries, only the last entry will be used. Sex entries of either full word or first letter are recognized (e.g. M or Male) -- matching is case insensitive.
Sex is used to change the formatting attributes in the pedigree to distinguish males, females, and individuals of unknown sex. BirthYear is converted to age in the current year under the assumption that all birthdays have passed this year and helps to direct the pedigree so older individuals are plotted above younger individuals.
relped produces a Graphviz-formatted file (directed or undirected, depending on input) with attributes deemed visually appropriate for building pedigrees. Unlike in a typically pedigree, all nodes at the same level in the plot may not be the same age, however all connections will be the same between runs of relped.
A single run of relped and Graphviz to produce a pedigree can be done as follows:
relped build \
--relatedness <relatedness> \
--demographics <demographics> \
--parentage <parentage> \
--output <output> \
&& dot -Tsvg -O <output>Important: How Graphviz plots a pedigree based on a single output from relped is not always visually appropriate for presenting your pedigree nework, therefore we recommend building multiple plots at once.
The below command template can be used to build multiple plots consecutively so that you may pick the most visually appropriate pedigree -- only the layout should change between runs, not the connections therefore all pedigrees should be equal short of visual fitness.
for run in {1..10}
do
relped build \
--relatedness <relatedness> \
--demographics <demographics> \
--parentage <parentage> \
--output $run-<output> \
&& dot -Tsvg -O $run-<output>
doneWhat the above does is loop through the numbers 1-10 (assigning the current number to run), then calls relped with your inputs (<relatedness>, <demographics>, and <parentage>) and writes multiple output files that are prepended with the run number ($run-<output>) -- then it calls Graphviz to produce rendered images in the format stated (note there is no space in -Tsvg).
We invite all contributors, please refer to CONTRIBUTING for further details.
This work is licensed under the the MIT License, see full terms of use in LICENSE file.