freebayes-snakemake

Example of a snakemake project

Installation

Download the repository from github

git clone https://github.com/LUMC/freebayes-snakemake.git

Install and activate the conda environment.

conda env create --file environment.yml
conda activate freebayes-snakemake

Settings priority

There are three levels where configuration options are set, in decreasing order of priority.

1. Flags passed to snakemake using --config, or in the specified --configfile.
2. Setting specified in the PEP project configuration, under the key freebayes-snakemake.
3. The default settings for the pipeline, as specified in the common.smk file.

Pipeline settings

The pipeline requires a single PEP configuration file, which specifies a csv sample table and a reference (example).

If you have multiple read pairs per sample, you can also specify a subsample table, with one line for each read pair (example).

Available settings

Option	Type	Explanation
reference	Required file	Indexed reference file to use with mapping and variant calling
capture_bed	Optional file	Add a section for picard CollectHsMetrics to the MultiQC report by specifying a capture bed file

Run the pipeline

Use the following commands to activate the conda environment for the pipeline, and run the example project configuration. This will create two output folders, sample1 and sample2, as well as a log folder that contains the log files from the pipeline.

conda activate freebayes-snakemake

snakemake --cores 1 --use-singularity --config pepfile=tests/pep/project_config.yaml

If you want to preserve the intermediate files of the pipeline, you can run Snakemake with the --notemp flag. Otherwise, all intermediate files will be removed when they are no longer needed.