Call CNVs from exome sequencing data

JACNEx calls germline Copy Number Variations (CNVs) from exome sequencing data.
The input data of this pipeline are Binary Alignment Maps (BAM) and Browser Extensible Data (BED) containing the intervals associated with the canonical transcripts.
For more information how obtaining the different files see https://github.com/ntm/grexome-TIMC-Primary

STEP 1 : Prepare the Environment

Before running JACNEx, ensure all dependencies are installed, and the environment is set up correctly.

STEP 2 : Run JACNEx

JACNEx.py orchestrates the entire pipeline, running the necessary steps to count fragments, cluster samples, and call CNVs. This involves the following steps:

1. Fragments Counting: Counts the number of sequenced fragments from each BAM file that overlap each exon.
   
2. Samples Clustering: Normalizes the counts, performs quality control on the samples, and forms the reference clusters.
   
3. Copy Number Calling: Determines parameters for CN0 and CN2 distributions, excludes non-interpretable exons, calculates likelihoods for each CN state, and applies a Continuous Hidden Markov Model (CO-HMM) to call and group CNVs.
   

The pipeline also handles intermediate results, quality control checks, and outputs the CNV calls in VCF format.

To run JACNEx.py, use the following command syntax:

BAMS="BAMs/sample1.bam,BAMs/sample2.bam"
BED="Transcripts_Data/ensemblCanonicalTranscripts.bed.gz"
WORKDIR="/path/to/workDir"

python JACNEx.py --bams $BAMS --bed $BED --workDir $WORKDIR 2> jacnex.log

CONFIGURATION:

DEPENDENCIES:

samtools

JACNEx needs samtools (tested with v1.15.1 - v1.18), can be installed with:

wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2
tar xfvj samtools-1.18.tar.bz2
cd samtools-1.18
./configure
make all all-htslib

You then need to place samtools-1.18/samtools in your $PATH (e.g. create a symlink to it in /usr/local/bin/ if you are sudoer), or pass it to JACNEx.py with --samtools= .

python

JACNEx needs python version >= 3.7 (3.6 and earlier have a bug that breaks JACNEx). For example on ALMA Linux 9 we use python3.12, available in the standard repos since ALMA 9.4:

sudo dnf install python3.12 python3.12-setuptools python3.12-numpy python3.12-scipy
sudo dnf install python3.12-pip-wheel python3.12-setuptools-wheel python3.12-wheel-wheel

python modules

JACNEx requires the following python modules:
numpy scipy numba ncls matplotlib scikit-learn KDEpy
On some distributions/environments you may also need to (re-)install setuptools. We recommend the following commands, which cleanly install all the requirements in a python virtual environment, using the system-wide versions if available:

PYTHON=python3.12 ### or python3, or python, or...
$PYTHON -m venv --system-site-packages ~/pyEnv_JACNEx
source ~/pyEnv_JACNEx/bin/activate
pip install --upgrade pip
pip install setuptools numpy scipy numba ncls matplotlib scikit-learn KDEpy

On an ALMA9.4 system today (28/05/2024) this uses the system-wide:
setuptools-68.2.2 numpy-1.24.4 scipy-1.11.1

(provided they are installed on the system), and it installs in ~/pyEnv_JACNEx/ :
numba-0.59.1 ncls-0.0.68 matplotlib-3.8.4 scikit_learn-1.4.2 KDEpy-1.1.9

You then need to activate the venv before running JACNEx, e.g.:

$ source ~/pyEnv_JACNEx/bin/activate
(pyEnv_JACNEx) $ python path/to/JACNEx/JACNEx.py --help