PCAWG Intra-Tumor Heterogeneity Simulations

This resource contains the simutated samples that go with the paper `Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes` which is available at the URL in the Related Links section below. Please find a full description of these data in the supplementary information of this paper, as well as the full author list and credit for creation of these data.

Please find below a description of the included files.

PhylogicNDT500:

Note difference between directories marked with and without "_all". It is recommended to not use files in "_all" directories, as they contain mutations below the detection limit of 3 variant reads.
* Copynumber: Segments/ directory - Subclonal copynumber is encoded via multiple reports of the same segment with a different CCF
* Variants: VCF/ directory - These follow PCAWG consensus basic read count annotations
* Purity/ploidy: PP_Table/ directory
* Truth clusters: Subclonal_Structure/ directory
* Truth assignments: Mut_Assign/ directory
* Truth mutations: Mafs_Real_Info/ directory

SimClone1000 - testing:
* Copynumber: *_segments.txt in each sample directory - There is no subclonal copynumber
* Variants: *.vcf - These follow PCAWG consensus basic read count annotations
* Purity/ploidy: Included purity_ploidy.txt file

SimClone1000 - truth:
* Every simulation has its own directory tree.
* Truth clusters (cluster position in CCF): [samplename]/simulated_0001/truth_tree/simulated_0001_subclonal_structure.txt
* Truth assignments: [samplename]/simulated_0001/truth_tree/simulated_0001_mutation_assignments.txt
* Truth mutations: [samplename]/simulated_0001/simulated_0001_0001/truth/simulated_0001_0001_multiplicity.txt