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==2.0.5

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.