Demo pipeline for testing different data chunking methods for MuTect2.
MuTect2 is a common tool used for variant calling of tumor-normal pairs. However, it is limited to running only in single-threaded mode, which can lead to extremely long execution times.
This demo pipeline uses different techniques to chunk the included list of target regions (targets.bed) into smaller segments to run in parallel, then aggregate all results for comparison to ensure that variant calls are the same across all chunking methods.
This pipeline comes pre-configured for usage on NYULMC's Big Purple HPC cluster using pre-built Singularity containers and pre-downloaded reference files.
In order to use this pipeline on your system you will need to update the file paths saved in nextflow.config for your system.
Singularity and Docker container recipes are included in the containers directory.
Paths to input .bam files for tumor and normal samples are read from the file samples.analysis.tsv.
Once correctly configured, the pipeline can be run with:
make run