Data

Tools

Indexes

Applications

Experiments

Open Source Science

vcftomaf

Nextflow pipeline to convert VCF files into MAF files.

https://github.com/qbic-pipelines/vcftomaf

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Nextflow pipeline to convert VCF files into MAF files.

Basic Info
  • Host: GitHub
  • Owner: qbic-pipelines
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage:
  • Size: 2.72 MB
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 5
  • Open Issues: 1
  • Releases: 3
Created over 2 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

qbic-pipelines/vcftomaf qbic-pipelines/vcftomaf

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

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. Optional Filtering of VCF files for PASS and / or 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:

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:

bash 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, Friederike Hanssen up to release 1.0.0. The pipeline was further developed by Famke Bäuerle after release 1.0.0.

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.

Owner

  • Name: QBiC (qbic-pipelines)
  • Login: qbic-pipelines
  • Kind: organization
  • Email: support@qbic.zendesk.com
  • Location: University of Tübingen

Bioinformatics analysis pipelines at QBiC

Citation (CITATIONS.md) 

# qbic-pipelines/vcftomaf: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [BCFTools](https://pubmed.ncbi.nlm.nih.gov/21903627/)

  > Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. PubMed PMID: 21903627; PubMed Central PMCID: PMC3198575.

- [vcf2maf](https://github.com/mskcc/vcf2maf)

> Cyriac Kandoth. mskcc/vcf2maf: vcf2maf v1.6.19. (2020). doi:10.5281/zenodo.593251

- [Maftools](https://github.com/PoisonAlien/maftools)

  > Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018 Nov;28(11):1747-1756. doi: 10.1101/gr.239244.118. Epub 2018 Oct 19. PMID: 30341162; PMCID: PMC6211645..

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [picard-tools](http://broadinstitute.github.io/picard)

- [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)

  > Li H, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719, doi: 10.1093/bioinformatics/btq671. PubMed PMID: 21208982. PubMed Central PMCID: PMC3042176.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
  • Create event: 2
  • Release event: 2
  • Issues event: 11
  • Watch event: 2
  • Member event: 1
  • Issue comment event: 33
  • Push event: 18
  • Pull request review comment event: 16
  • Pull request review event: 27
  • Pull request event: 38
Last Year
  • Create event: 2
  • Release event: 2
  • Issues event: 11
  • Watch event: 2
  • Member event: 1
  • Issue comment event: 33
  • Push event: 18
  • Pull request review comment event: 16
  • Pull request review event: 27
  • Pull request event: 38

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 2
  • Total pull requests: 12
  • Average time to close issues: 10 months
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.17
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 12
  • Average time to close issues: N/A
  • Average time to close pull requests: about 14 hours
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.17
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • famosab (4)
  • FriederikeHanssen (2)
  • allyssonallan (1)
Pull Request Authors
  • famosab (17)
  • FriederikeHanssen (8)
  • allyssonallan (1)
Top Labels
Issue Labels
enhancement (3) bug (2)
Pull Request Labels
bug (1)

Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/multiqc/meta.yml cpan
pyproject.toml pypi
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • eWaterCycle/setup-singularity 931d4e31109e875b13309ae1d07c70ca8fbc8537 composite
  • nf-core/setup-nextflow v1 composite
modules/nf-core/bcftools/concat/meta.yml cpan
modules/nf-core/bcftools/view/meta.yml cpan
modules/nf-core/gunzip/meta.yml cpan
modules/nf-core/picard/liftovervcf/meta.yml cpan
modules/nf-core/tabix/tabix/meta.yml cpan
modules/nf-core/untar/meta.yml cpan
modules/nf-core/vcf2maf/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml cpan
Dockerfile docker
  • nfcore/base 2.1 build
environment.yml pypi
modules/nf-core/bcftools/concat/environment.yml pypi
modules/nf-core/bcftools/view/environment.yml pypi
modules/nf-core/gunzip/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
modules/nf-core/picard/liftovervcf/environment.yml pypi
modules/nf-core/tabix/tabix/environment.yml pypi
modules/nf-core/untar/environment.yml pypi
modules/nf-core/vcf2maf/environment.yml pypi