fastclone-guanlab 1.0.3

An inference tool for tumour subclonal composition

FastClone

FastClone is a fast algorithm to infer tumour heterogeneity. Given somatic mutation frequencies and copy number data, FastClone infers subclonal composition and phylogeny. The algorithm won the first place in DREAM Somatic Mutation Calling -- Heterogeneity Challenge in 2016.

Installation

FastClone needs Python 3.5 or later version. It needs logbook, python-fire, scikit-learn, and pandas. To install the package using Pip,

git clone https://github.com/GuanLab/FastClone_GuanLab.git
pip install FastClone_GuanLab/

(Please make sure you have the slash at the end, which forces pip to install from local directory, otherwise it will run into error)

You also can directly pip install FastClone with the command below.

pip install fastclone-guanlab

Usage

FastClone accepts either MuTect VCF + Battenberg format (specified in the DREAM SMC-Het Challenge) or PyClone format.

The general format of the command line:

fastclone load-[FILE_FORMAT] prop [FILE_NAME] [TUMOR_PURITY] solve [OUTPUT_PATHWAY]

An example to load samples and infer (t1.tsv is included in this repository):

fastclone load-pyclone prop t1.tsv 0.8 solve ./fastclone_result

（Please make sure t1.tsv is under your current directory）

Run fastclone for more help information.

If MuTect VCF and PyClone samples are provided, note that MuTect mutations are labelled as 'Chromosome:Coordinate:AltBase', such as 'Y:15989697:G'. Make sure PyClone ID uses the same ID.