Clonal dynamics after allogeneic haematopoietic cell transplantation using genome-wide somatic mutations

These are large files need to reproduce analysis in the manuscript "Clonal dynamics after allogeneic haematopoietic cell transplantation using genome-wide somatic mutations". These files are to be used alongside the code and smaller data files available at:
https://github.com/mspencerchapman/Clonal_dynamics_of_HSCT
The folders 'annot_files' and 'annot_files_no_dups' should be placed in the 'data' folder from the github repository.
The contents of the folder 'Targeted_sequencing_data' should be placed in the 'data/Targeted_sequencing_data' folder from the github repository. Note that the 'raw_model_output' data is not essential for most analyses as the 'posterior_cell_fracs.Rds' object is a combined and processed list of this data. To reproduce the phylogeny-aware targeted sequencing results from the Gibb's sampler, you will need to download the compressed data in 'Targeted_sequencing_data/data_by_baitset'.
The HDP_multi_chain.Rdata file should be placed in the data/HDP folder
The folder 'genomic_loci_reference_files' (which is 8.5Gb when uncompressed) is only needed for one analysis to create Extended Data Fig. 5c. and therefore need only be downloaded if trying to reproduce this analysis. If used, it should again be place in the 'data' folder of the github repository.