Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

This repository contains code corresponding to analysis reported in <a href="https://www.cell.com/cell/fulltext/S0092-8674(21)00294-4">Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes</a>

The submodules in this repository link to the version of the code that was used to produce the results and are provided as a permanent archive.

Some of the methods may see further development, therefore, if you're interested in applying a method it is encouraged to go to the linked repositories and check out the latest version there.

Data from the Pan-Cancer Analysis of Whole Genomes project (PCAWG) is available here, including consensus copy number profiles and consensus subclonal architectures.

Contents

| Repository | Description | | --- | --- | | CICC | Method to construct a consensus subclonal architecture | | CSR | Method to construct a consensus subclonal architecture | | SimClone1000 | Pipeline that created the SimClone1000 simulated data set | | icgc_consensus_copynumber | Pipeline that constructs the consensus copy number profiles | | icgc_consensus_purity | Pipeline that establishes a consensus purity estimate | | icgc_consensus_clustering_assignment | Pipeline that assigns all SNVs, indels and SVs to consensus mutation clusters | | MutationTimeR | Version of MutationTimeR used to assign mutations to clusters | | weme | Method to construct a consensus subclonal architecture | | SpoilSport | Method to correct cluster positions and sizes for missed SNVs (i.e. winner's curse) |

Dependencies

Each of the above named repositories contains a description of the depencies required for that component.

Used input methods

Copy number

• ABSOLUTE - code - paper
• Aceseq - code - paper
• Battenberg - code - paper
• cloneHD - code - paper
• JaBbA - code - paper
• Sclust - code - paper

Subclonal architecture

• Bayclone - code - paper
• Ccube - code - paper
• CliP - code - paper
• cloneHD - code - paper
• CTPSingle - code - paper
• DPClust - code - paper
• PhylogicNDT - code - paper
• PhyloWGS - code - paper
• Pyclone - code - paper
• Sclust - code - paper
• SVclone - code - paper

Other

• TrackSig - code - paper
• MutationTime.R - code - paper