qbic-pipelines/vcftomat

Introduction

qbic-pipelines/vcftomat 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. Merges all vcfs from the same sample with bcftools/merge (bcftools)
4. Converts the (merged) vcfs to a matrix using a custom R script written by @ellisdoro (R)
5. 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:

sample,gvcf,vcf_path,vcf_index_path
SAMPLE-1,false,path/to/vcf.gz,path/to/.vcf.gz.tbi
SAMPLE-1,false,path/to/vcf.gz,path/to/.vcf.gz.tbi
SAMPLE-2,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi

Each row represents a VCF file coming from a sample. 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:

nextflow run qbic-pipelines/vcftomat \
   -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/vcftomat 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

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.