qbic-pipelines/variantconsensus

Introduction

qbic-pipelines/variantconsensus is a bioinformatics pipeline that combines results from multiple variant callers to find a consensus VCF.

Inspired by

Trevarton, A. J., Chang, J. T., & Symmans, W. F. (2023). Simple combination of multiple somatic variant callers to increase accuracy. Scientific reports, 13(1), 8463.

1. Split provided VCFs into SNPs and INDELS (bcftools/view)
2. Intersect SNPs / INDELs keeping only variants found in at least (N-1) / 2 of the provided VCFs (bcftools/isec)
3. Filter the consensus VCF for variants marked as 'PASS,.' (bcftools/view)
4. Report statistics for the filtered consensus VCFs (bcftools/stats)
5. Present statistics for variants (MultiQC)

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

patient,sample,variantcaller,vcf,vcf_tbi,varianttype
A,t5,strelka,https://github.com/qbic-pipelines/test-datasets/raw/refs/heads/main/variantconsensus/tumor_5_vs_normal_5.strelka.somatic_indels_VEP.ann.vcf.gz,https://github.com/qbic-pipelines/test-datasets/raw/refs/heads/main/variantconsensus/tumor_5_vs_normal_5.strelka.somatic_indels_VEP.ann.vcf.gz.tbi,indels

Each row represents a VCF file and its index. The varianttype can be either snps, indels or both.

Now, you can run the pipeline using:

nextflow run qbic-pipelines/variantconsensus \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

qbic-pipelines/variantconsensus was originally written by Famke Bäuerle.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

If you use qbic-pipelines/variantconsensus for your analysis, please cite it using the following doi: 10.5281/zenodo.17100035

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.