qbic-pipelines/vcftocounts

Introduction

qbic-pipelines/vcftocounts is a bioinformatics pipeline that processes g.vcf files to a matrix suitable for downstream analysis. The pipeline is built using Nextflow and processes data using the following steps:

1. Indexes (g.)vcf files (tabix)
2. Converts g.vcf files to vcf with genotypegvcf (GATK)
3. Filters the VCF based on a string given to the filter param with bcftools/view (bcftools) - Turned off by default.
4. Concatenates all vcfs that have the same id and the same label with bcftools/concat (bcftools)
5. Changes the sample name in the vcf file to the filename with bcftools/reheader (bcftools) - This can be turned off by adding --rename false to the nextflow run command.
6. Merges all vcfs from the same sample with bcftools/merge (bcftools)
7. Removes entries in the ID column with bcftools/annotate (bcftools) - his can be turned off by adding --removeIDs false to the nextflow run command.
8. Converts the (merged) vcfs to a matrix using a custom R script written by @ellisdoro (R)
9. Collects all reports into a MultiQC report (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:

csv sample,label,gvcf,vcf_path,vcf_index_path SAMPLE-1,pipelineA-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi SAMPLE-1,pipelineB-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi SAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi SAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi

Each row represents a VCF file coming from a sample. The label column enables concatenation of vcfs (for example when the pipeline produces different vcfs for chrM and chrY). The gvcf column indicates whether the file is a g.vcf file or not. The vcf_path and vcf_index_path columns contain the path to the VCF file and its index, respectively.

Now, you can run the pipeline using:

bash nextflow run qbic-pipelines/vcftocounts \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --genome GATK.GRCh38 \ --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/vcftocounts was originally written by Famke Bäuerle, Dorothy Ellis.

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/vcftocounts for your analysis, please cite it using the following doi: 10.5281/zenodo.14616650

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.