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raphael-group / hatchet2-paper

Publication repository for results that accompany the HATCHet2 paper.

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HATCHet is an algorithm to infer haplotype- and clone-specific copy-number aberrations (CNAs), clone proportions, and whole-genome duplications (WGD) for several tumor clones jointly from one or more bulk tumor samples from the same patient. HATCHet2 is implemented in the HATCHet repository (versions 1.1+): https://github.com/raphael-group/hatchet

Overview

This repository contains supporting data for the results that accompany the HATCHet2 paper. It contains HATCHet2 results on the following datasets:

  • hatchet2-sim-results: MASCoTe simulated datasets from the original HATCHet paper (available in the HATCHet publication repository)
  • gundem: 50 whole-genome sequencing samples in total from 10 patients with prostate cancer from the Gundem et al., 2015 study. Data availability is described in the original publication.
  • 10x: m10x Genomics single-cell breast cancer dataset: about 10500 cells total from low-coverage single-cell whole-genome sequencing from 5 sections of a breast tumor. Described in an application note on the 10x website.

This repository also contains HATCHet results on the MASCoTe simulated data in hatchet-sim-results, run with parameters set to match HATCHet2 as closely as possible.

Directory contents

Each directory corresponding to a single individual contains:

About

Publication repository for results that accompany the HATCHet2 paper.

License:BSD 3-Clause "New" or "Revised" License