54gene workflow: 54gene WGS germline

This workflow is designed to take either fastqs or gvcfs as input, and emit a joint-called multi-sample VCF. Please see Read the Docs for additional documentation.

You can find a small test dataset and pre-configured files for this pipeline here.

Authors

• Esha Joshi
• Cameron Palmer
• Bari Jane Ballew (@bballew)

Usage

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository.

Step 1: Obtain a copy of this workflow

Clone this repository to your local system, into the place where you want to perform the data analysis.

    git clone [email protected]:data-analysis5/54gene-wgs-germline.git

Step 2: Configure workflow

The pipeline inputs include:

• A configuration file
• A manifest file
• A list of intervals
• A sex linker file
• A MultiQC config file (provided)

Step 3: Install the run-time environment

If needed, install miniconda by following the steps here.

• Create a conda environment with, minimally, the dependencies defined in environment.yaml.

# create the env
conda env create -f environment.yaml

Step 4: Execute workflow

Activate the conda environment:

conda activate 54gene-wgs-germline

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

To run the pipeline in a cluster environment, edit wrapper.sh as needed for your system, and then run via

bash run.sh

Alternatively, you may run snakemake pipelines on a cluster via something like this

snakemake --use-conda --cluster sbatch --jobs 100

Step 5: Investigate results

Upon pipeline completion, verify that all steps have completed without error by checking the top-level Snakemake log. The bottom few lines of should contain something like nnn of nnn steps (100%) done. Additional job logs (when run on a cluster) are stored in the logs/ directory.

All pipeline results are stored in the results/ directory.

The hard-filtered, joint-called VCF can be found in results/HaplotypeCaller/filtered/HC_variants.hardfiltered.vcf.gz.

For future joint-calling, the gVCFs are located at results/HaplotypeCaller/called/<sample>_all_chroms.g.vcf.gz.

Deduplicated and post-BQSR bams are found at results/bqsr/<sample>.bam.