Cell-free DNA analysis toolkit
This is a Python package for easy and efficient cell-free DNA analysis.
All citations should reference to original paper.
Install
If you dont already have numpy and scipy installed, it is best to download
Anaconda, a python distribution that has them included.
https://continuum.io/downloads
Create environment and pip install:
conda create -n cfdna python=3.11.3
conda activate cfdna
pip install cfdna
Dependencies can be installed by:
pip install -r requirements.txt
PyPI install, presuming you have all its requirements installed:
pip install cfdna
Usage
import cfdna as cf
import numpy as np
# Create data
cfdata = cf.cfDNA()
frags = cf.io.readBAM("test.bam")
# Call CNVs
cf.proc.call_cnv_pipline(cfdata, frags)
# Plot CNVs
cf.pl.plot_cnv(cfdata, "test.bam")
Run from the commadline:
python -m cfdna callCNVs --bam test.bam --segs --genome hg19 --bin_size 100000
This will output a .png plot and seg file.
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