These are the post-mapache bash scripts used to perform analyses in the paper of Psonis et al. 2024 https://doi.org/10.1016/j.fsigen.2024.103060. They are separated into two main pipelines, one fo the living relatives (to be performed first) and a second for the victims.
The scripts are provided for the shake of reprodusability of the results, but also for free use by the scientific community. Note though that I do not intend to maintain this repository and hence I may not reply to reporting issues.
I also include the samplelist and the two config files of mapache (for the two runs, with and without bamutil).