Python implementation of Chimaera algorithm based on Inferring clonal composition from multiple tumor biopsies.
The supplementary tables for the publication can be found here.
If you use Chimaera please cite it using the following:
@article{manica2020inferring,
title={Inferring clonal composition from multiple tumor biopsies},
author={Manica, Matteo and Kim, Hyunjae Ryan and Mathis, Roland and Chouvarine, Philippe and Rutishauser, Dorothea and Roditi, Laura De Vargas and Szalai, Bence and Wagner, Ulrich and Oehl, Kathrin and Saba, Karim and others},
journal={NPJ systems biology and applications},
volume={6},
number={1},
pages={1--13},
year={2020},
publisher={Nature Publishing Group}
}- Python >=3.5
- pip >= 10.0
NOTE: For Python >=3.7 make sure Cython is installed before the installation of chimaera: pip install Cython.
In case pip is installed just type:
pip install .or directly from the repository. Using ssh authentication:
pip install git+ssh://git@github.com/drugilsberg/chimaeraUsing https:
pip install git+https://github.com/drugilsberg/chimaera.gitChimaera come with an excutable called chimaera that can be used as follows:
chimaera /path/to/data.txtIt accepts different arguments, read the help for a full description:
usage: chimaera [-h] [--output-path OUTPUT_PATH]
[--min-clone-size MIN_CLONE_SIZE]
[--clone-analyzer CLONE_ANALYZER] [--input-sep SEP]
[--allele-cn-lb DELTA_LB] [--allele-cn-ub DELTA_UB]
[--log-file LOG_FILE] [--version]
input_file
Run chimaera to estimate clonal composition of a tumor using multiple biosies
from a single patient.
positional arguments:
input_file File containing mutations data in tabular format. It
needs an header including VAF and CN fields(case-
insensitive) together with a sample-id, e.g.: id1-VAF
id1-CN ... idn-VAF idn-CN. An index containing the
mutations id is also required.
optional arguments:
-h, --help show this help message and exit
--output-path OUTPUT_PATH
Path to directory where chimaera results should be
saved. If not passed it will print the output to
stdout (it can be used for piping commands).
--min-clone-size MIN_CLONE_SIZE
Minimum number of mutations needed to consider a
clone. Default to 5.
--clone-analyzer CLONE_ANALYZER
Clone analyzer used for optimizing clone frequencies.
Default to random. If robust is used it gives stable
estimates accross multiple run. Method random does not
underestimate frequencies but results are less
repeatable (~0.05-0.1 variability accross runs in
frequency estimates).
--input-sep SEP Field separator for input_file. Default to tab.
--allele-cn-lb DELTA_LB
Allele copy number lower bound. Default to 0.0.
--allele-cn-ub DELTA_UB
Allele copy number upper bound. Default to 4.0.
--log-file LOG_FILE File for logging chimaera output. Unless specified no
logging of chimaera execution is produced.
--version, -v chimaera versionSee the file data/exome_sample_data.txt for an example of the input format.
Run the example:
chimaera data/exome_sample_data.txtThe Chimaera web-service has been deprecated in favour of the python package hosted in this repository. Please check the examples to use Chimaera in your research.