GDAN HCMI Project: Driver event concordance pipeline

Overview

This project is part of the Genomic Data Analysis Network (GDAN) initiative within the Human Cancer Models Initiative (HCMI). The primary goal is to assess the concordance of driver mutations between paired tumor and tumor-model whole genome sequencing (WGS) samples.

Usage

Configuration

• Before running the pipeline, ensure that the copy number data, SNV/indel data, and TCGA data are downloaded into directories of your choice.
• Next, edit pipeline/config.yaml to map the input large data files correctly.
• If you want to start from the point where the copy number and mutation data are already compiled, you can use this synapse link (https://www.synapse.org/Synapse:syn71463818) to access h5ad files for the concordance calculation.

Install python dependencies

The pipeline also requires snakemake, so you must make sure it's correctly installed (either through mamba or pip).

pip install -r requirements.txt
cd pysrc/
pip install .
cd ../pipeline/  # run pipeline within pipeline/ directory

Pipeline structure

This snakemake pipeline is structured as shown in the following graph:

Pipeline run command

Make sure snakemake is installed in your environment before proceeding.

1. Running in a cluster

The following script assumes you are using SLURM as your job distributor.

SLURM_PARTITION=componc_cpu
CLUSTER_FMT="sbatch --partition=$SLURM_PARTITION --cpus-per-task={threads} --mem={resources.mem_mb} --job-name={rule}.{wildcards} --error=logs/{rule}/{rule}.{wildcards}.%j.err --output=logs/{rule}/{rule}.{wildcards}.%j.out --time=24:00:00"
cmd="snakemake --executor cluster-generic"
cmd="$cmd --cluster-generic-submit-cmd \"$CLUSTER_FMT\""
cmd="$cmd --profile profile/"
cmd="$cmd --singularity-args \"--cleanenv --bind /path/to/data\""
cmd="$cmd -p"
cmd="$cmd --jobs 600"
cmd="$cmd --configfile config.yaml"
cmd="$cmd --use-singularity"
eval $cmd

2. Running locally

You could also run the pipeline in a single node.

cmd="snakemake "
cmd="$cmd --singularity-args \"--cleanenv --bind /path/to/data\""
cmd="$cmd -p"
cmd="$cmd --jobs 50"
cmd="$cmd --configfile config.yaml"
cmd="$cmd --use-singularity"
eval $cmd

Contact

For questions, please feel free to reach out to Seongmin Choi ([email protected]).