GeneDrop

What is this?

GeneDrop is a tool for simulating the breeding of diploid organisms with known linkage maps.

Attribution

Feel free to use this in any way you see fit, as long as you attribute me. If you use this in scientific work, then please cite the paper in which we introduce GeneDrop (https://www.sciencedirect.com/science/article/pii/S2212066116300321).

What's new?

If you've used the old versin of GeneDrop then the following features are new,

• Support for overlapping generations
• Support for individuals in different generations having the same ID (use the new :: syntax in the pedigree)
• Multiallelic loci. Alleles can be now specified as any string that doesn't include a comma.

How do I use it?

You can either build from source or use one of the prebuilt binaries.

Program versions

There is both a graphical version (GeneDropGUI.exe) and command line version (GeneDrop.exe). The use of the graphical version should be self-explanatory and the available options for the command line version can be obtained via GeneDrop.exe --help.

Input files

GeneDrop takes three input files, each of which is formatted as CSV. Each file should have a header, with columns described as follows.

Loci files

This describes the loci to be tracked in the simulations.

Column	Meaning
Locus ID	An identifier for a given locus
Distance (cM)	The genetic distance in centimorgans from one end of the chromosome
Chromosome	Which chromosome the locus sits on

An example loci file might look like,

Locus ID	Distance (cM)	Chromosome
L1	0	A
L2	0.3	A

The above examples describes two loci which both sit on chromosome A. L1 sits on the end of the chromosome and L2 sits 0.3 centimorgans from L1.

Founder files

This describes the genotypes of the founding individuals in the pedigree.

Column	Meaning
Founder	The name of the founding individual, can take an arbitrary value.
...	Columns named after the loci described in the loci file. These give the genotype of the founding individual.

Arbitrary allele names can be used in the genotype columns, and slashes are used to indicate heterozygosity. An example founder file might look like,

Founder	L1	L2
A	0	1
B	1/0	0

The above examples describes founders A and B in terms of their genotype at loci called L1 and L2. Founder A carries the 0 allele at L1 and the 1 allele at L2. Founder B is heterozygous at the L1 locus and carries the 0 allele at L2.

Pedigree files

This describes the pedigree to be simulated. Each row describes an individual in the pedigree.

Column	Meaning
Generation	The name of the generation the individual belongs to, can take an arbitrary value.
ID	A specifier for the individual. Arbitrary but must be unique within a generation.
P1	Specifier for first parent of this individual.
P2	Specifier for second parent of this individual.

If IDs are unique they can be used as a specifier. If IDs are not unique, then one can use the format <generation name>::<ID>. One can also refer to founder individuals using the IDs specified in the founders file. An example pedigree file might look like,

Generation	ID	P1	P2
F1	C	A	B
F1	D	A	B
F2	E	C	D

The above example describes a F2 cross where A and B are founder individals described in the founders file.

Building from source

The project is set up to use cmake to allow cross-platform compilation. First ensure you have cmake, Boost and your C++ compiler of choice installed on your system.

1. If you plan to build the Qt front-end then cmake needs to know where to find it. It will attempt to do this automatically, but if it fails (or you want to use a particular Qt installation) you need to set the CMAKE_PREFIX_PATH variable in the top-level CMakeLists.txt to point to the install directory for Qt.
2. Make a directory called build, cd into it and call cmake .. to generate a build directory with files appropriate for your system. Future rebuilds of the files can be run by targetting the build directory with cmake. Only the initial build needs to be called from that directory but targetting the top level directory.
3. Compile from the files generated in the build directory. This can be done in with compiler of choice or through cmake directly with cmake --build ..

Typical issues

1. cmake assumes you are targetting x86. You can switch architecture by editting the generated files for your given compiler. For MSVC this may not work correctly on first try, make sure that the project property files are not also specifying the target architecture in the additional compiler options. In MSVC 2017 this option can be found under Properties > Librarian > All Options (for Backend) or Configuration Options > Linker > All Options (for other projects). You may also have to update the output directory for the Backend shared library (Properties > General > Output Directory) and linker input directories for the other projects (Properties > Linker > General > Additional Library Directories).

Project structure

Project Name	Function
GeneDropBackEnd	Does all simulations, compiles to static library
GeneDropCommandLineFrontEnd	Command line interface for using the back end
GeneDropTests	A test suite ensuring the program works as intended (uses Catch )
GeneDropGraphicalFrontEnd	Graphical interface for using the back end (uses Qt )