See pipeline.md for a detailed documentation of all analyses done, except Jaatha, which is documented in jaatha_scripts/Rscripts/README.md. All scripts are stored in the folder scripts. Intermediate files (such as the input files for Fastsimcoal) are stored in respective subfolders with the scripts
All analyses are conducted using clusters BioHPC, CoolMUC-2 and the interactive web AI server hosted by Leibniz Rechenzentrum (LRZ). pipeline.md written by Chyiyin Gwee; code for jaatha analyses by Dirk Metzler
pipeline.md in the following order (link to scripts):
- Raw data processing: trim, map , rmdup, mapDamage, ploidy
- Variant calling: ANGSD, SAMtools, GATK, overlap, paralog, pop files
- Combine invariant sites and the final set of variant sites
- PCA
- Admixture: plot
- Admixtools2: input files
- Dsuite: input files
- Summary statistics: TajD, FST, Dxy, Da, Pi, plot, pop files
- Neutral sites: variant, invariant
- MSMC2: input
- Stairway plot: SFS, blueprints
- SMC++
- Fastsimcoal2: SFS, parameter estimation, plot, simulate SFS from estimates, bootstrap, input files
- TWISST: input files
- Fastsimcoal to TWISST: simulate trees, twisst, input files
Gwee, C.Y., Metzler, D., Fuchs, J. and Wolf, J.B.W. (2025), Reconciling Gene Tree Discordance and Biogeography in European Crows. Mol Ecol, 34: e17764. https://doi.org/10.1111/mec.17764