https://github.com/stevekm/mutect2_target_chunking
demo pipeline for testing different data chunking methods for MuTect2
https://github.com/stevekm/mutect2_target_chunking
mutect2 nextflow variant-calling
Last synced: 4 months ago
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demo pipeline for testing different data chunking methods for MuTect2
- Host: GitHub
- URL: https://github.com/stevekm/mutect2_target_chunking
- Owner: stevekm
- Created: 2019-07-02T17:40:07.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-07-02T17:53:26.000Z (almost 7 years ago)
- Last Synced: 2025-06-13T20:06:08.053Z (12 months ago)
- Topics: mutect2, nextflow, variant-calling
- Language: Nextflow
- Size: 158 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# MuTect2 Target Chunking
Demo pipeline for testing different data chunking methods for MuTect2.
[MuTect2](https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php) 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.
# Usage
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
```