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https://github.com/cbg-ethz/scsommerclock

Test for a molecular clock based on the phylogenetic tree inferred from single-cell DNA sequenzing data

https://github.com/cbg-ethz/scsommerclock

Science Score: 23.0%

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Keywords

cancer-genomics molecular-clock neutrality-test scdnaseq
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Test for a molecular clock based on the phylogenetic tree inferred from single-cell DNA sequenzing data

Basic Info
  • Host: GitHub
  • Owner: cbg-ethz
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 2.21 MB
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  • Stars: 6
  • Watchers: 4
  • Forks: 0
  • Open Issues: 1
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cancer-genomics molecular-clock neutrality-test scdnaseq
Created about 4 years ago · Last pushed about 3 years ago
Metadata Files
Readme License

README.md

Single-Cell SOMatic MolEculaR Clock testing

This repo contains a Poisson Tree (PT) Test for the existence of a somatic clock in single-cell phylogenies. In short, it tests if different cell lineages evolve at a similar rate, accumulating mutations according to a molecular clock. As input the test requires a mutation matrix, a phylogeny of contemporaneously sampled cells, and error rates.

This repo contains scripts for running - the PT Test - and, in a subfolder (AnalysisPipelines), scripts for - the processing of real scDNA-seq data - the analysis of real scDNA-seq data - the simulation of scDNA-seq data (via coalescent) - the analysis and plotting of simulated scDNA-seq data

Installation

Requirements

  • python3.X:
    • ete3
    • numpy
    • pandas
    • scipy

The requirements cant be installed using pip: bash python -m pip install ete3 pandas scipy

Usage

The PT test can be run with the following shell command: bash python run_PT_test.py <VCF_FILE> <NEWICK_TREE_FILE> [-o] [-excl] [-incl] [-w] [-FN] [-FP]

Input files

The PT test requires two input files: - Called variants in VCF format (VCF info), where each sample is a cell - An inferred phylogenetic tree in newick format (cell names need to be the same as in the VCF).

Note

Trees can be inferred, for example, with CellPhy or infSCITE; both outputs are compatible with the PT test

Optional Arguments

  • -o <str>, Output file. Default = .poissonTree_LRT.tsv.
  • -excl <str>, Regex pattern for samples/cells to exclude. Default = none.
  • -incl <str>, Regex pattern for samples/cells to include. If set, only these samples/cells are included. Default = all cells.
  • -w <list of int>, Maximum weight values. Default = 100, 200, ..., 1000'.
  • -FN <float>, Estimated FN rate (for CellPhy and infSCITE: inferred from .log/stdout file).
  • -FP <float>, Estimated FP rate (for CellPhy and infSCITE: inferred from .log/stdout file).

Example

To run the PT test on the simulated data in the example_data folder, execute bash python run_PT_test.py example_data example_data/data_simulated_clock.vcf.gz example_data/data_simulated_clock.raxml.bestTree or bash python run_PT_test.py example_data example_data/data_simulated_noclock.vcf.gz example_data/data_simulated_noclock.raxml.bestTree

The former data is simulated under a molecular clock, the later with a deviation from the clock (evolutionary rate amplified by 5x in a subtree)

Note

FN and FP rate are inferred from the .raxml.log file

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

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