Genotyping Uncertainty with Sequencing data and linkage MAPping (GUSMap).
An R package for performing linkage mapping using low and/or high coverage sequencing data without requiring filtering with respect to read depth.
The easiest way to install GUSMap in R is using the devtools package.
install.packages("devtools")
devtools::install_github("tpbilton/GUSbase")
devtools::install_github("tpbilton/GUSMap")
Note: Some of the functions are coded in C and therefore an appropriate C compiler is needed for the package to work. For windows OS, Rtools (https://cran.r-project.org/bin/windows/Rtools/) provides a compiler.
There are three different types of mapping populations that are available GUSMap can handle. There is a tutorial for each of these mapping populations explaining how to use GUSMap to construct linkage maps.
- A back-cross (BC) population. See the BC Introduction tutorial.
- A full-sib family. See the FS Introduction tutorial.
- An intercross/F2 (IC) population. See the IC Introduction tutorial.
Please note that GUSMap is not suitable for recombinant inbred lines (RILs) populations.
This package is under continued development. If you have any suggests for improvement or additional features you like to see, I'd suggest posting a question under the Issues. I'm also happy for people to suggest changes via a pull request provided it fits within the favour of the package.
To cite this R package:
Bilton, T.P., Schofield, M.R., Black, M.A., Chagné, D., Wilcox, P.L., & Dodds, K.G. (2018). Accounting for errors in low coverage high-throughput sequencing data when constructing genetic maps using biparental outcrossed populations. Genetics, 209(1), 65--76. doi:10.1534/genetics.117.300627
The initial development of this package was partially funded by the Ministry of Business, Innovation and Employment via its funding of the “Genomics for Production & Security in a Biological Economy” programme (Contract ID C10X1306).