Introduction

qbic-pipelines/vcftomaf is a bioinformatics pipeline that converts input Variant Call Format (vcf) files with one or two columns of (paired) samples to tabular Mutation Annotation Format (maf). The resulting file(s) can be analyzed singly or as an entire cohort in R with maftools.

1. Filtering VCF files for PASS and optionally with a target bed file (BCFtools)
2. Optional liftover (needs a chain file, --fasta should refer to target genome version) (Picard LiftOverVCF)
3. Conversion from vcf to maf format(vcf2maf)
4. Collect QC metrics and versions (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:

sample,normal_id,vcf_normal_id,tumor_id,vcf_tumor_id,vcf,index
mutect2_sample1,SAMPLE123,PATIENT1_SAMPLE123,SAMPLE456,PATIENT1_SAMPLE456,/path/to/vcf,/path/to/tbi
test2,control2,NORMAl,,,/path/to/vcf,/path/to/tbi

Each row represents a sample with one or two columns in the VCF file. The normal_id and tumor_id will be used for naming the columns in the MAF file. The vcf_normal/tumor_id refers to the sample name in the VCF file. This differs for each caller. For VCFs obtained from nf-core/sarek, the following is tested:

Caller	Normal ID	Tumor ID
Manta	NORMAL	TUMOR
Mutect2	{patient}{_sample}	{patient}{_sample}
Strelka2	NORMAL	TUMOR

The values for patient and sample can be obtained from the nf-core/sarek samplesheet.

Now, you can run the pipeline using:

nextflow run qbic-pipelines/vcftomaf \
   -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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

For more details about the output files and reports, please refer to the output documentation.

Credits

qbic-pipelines/vcftomaf was originally written by SusiJo and Friederike Hanssen

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/vcftomaf for your analysis, please cite it using the following doi: 10.5281/zenodo.10812762

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

This pipeline is based on code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license. The pipeline is currently maintained at QBiC and not an nf-core pipeline since it has not undergone nf-core community review.

You can cite the nf-core publication as follows:

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.