variantcatalogue

Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

https://github.com/nf-core/variantcatalogue

Science Score: 54.0%

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 11 DOI reference(s) in README
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Academic publication links
Links to: biorxiv.org
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JOSS paper metadata
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Low similarity (11.3%) to scientific vocabulary

Keywords

nextflow nf-core pipeline workflow

Last synced: 6 months ago · JSON representation ·

Repository

Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: dev
Homepage: https://nf-co.re/variantcatalogue
Size: 184 MB

Statistics

Stars: 9
Watchers: 158
Forks: 4
Open Issues: 3
Releases: 0

Topics

nextflow nf-core pipeline workflow

Created about 3 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Introduction

nf-core/variantcatalogue is a bioinformatics best-practice analysis pipeline for Workflow designed to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Pipeline summary

A. Mapping subworkflow 1. Index the reference genome (BWA index) 2. Trim the reads (Trimmomatic) 3. Align the reads (BWA mem) 4. Index the aligned bam files (Samtools index) 5. Read QC (FastQC) 6. Coverage calculation (Mosdepth) 7. Alignemnt QC (Picard Collect WGS metrics) 8. Alignemnt QC (Picard Collect Alignment Summary Metrics) 9. Alignemnt QC (Quality Scores distribution) 10. Present QC for raw reads (MultiQC)

B. SNV/Indel subworkflow 1. Variant calling (DeepVariant) 2. Joint calling (GLnexus) 3. Split multi-allelic variants (Bedtools norm) 4. Redefine varaints ID (Bedtools Annotate) 5. Sample QC and sex inference (Hail) 6. Variant QC and frequency calculation (Hail) 7. Annotation (VEP)

C. Mitochondrial Subworkflow 1. Index the mitochondrial reference genome (BWA index) 2. Index the shifted mitochondrial reference genome (BWA index) 3. Extract the reads mapping to the MT chromosome (GATK) 4. Revert the sam to a fastq file (GATK) 5. Align the reads against the mitochondrial reference genome (BWA mem) 6. Align the reads against the shifted mitochondrial reference genome (BWA mem) 7. Index the aligned bam files (Samtools index) 8. Mark duplicates (GATK) 9. Colect HS metrics (Picard) 10. Call variants with Mutect2 (GATK) 11. Liftover the variants mapped against the shifted reference genome (GATK) 12. Merge the VCFs files (GATK) 13. Variant QC and frequency calculation (Hail)

D. Structural varaint subworkflow May be included soon

Quick Start

Install Nextflow (>=22.10.1)
Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).
Download the pipeline and test it on a minimal dataset with a simple three lines command:

wget https://github.com/scorreard/Variant_catalogue_pipeline/blob/main/testdata/reference/hg38_full_analysis_set_plus_decoy_hla_chr20_X_Y_MT.fa.gz?raw=true gzip -d hg38_full_analysis_set_plus_decoy_hla_chr20_X_Y_MT.fa.gz > hg38_full_analysis_set_plus_decoy_hla_chr20_X_Y_MT.fa bash nextflow run nf-core/variantcatalogue -profile test,YOURPROFILE --outdir <OUTDIR>

Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (YOURPROFILE in the example command above). You can chain multiple config profiles in a comma-separated string.

The pipeline comes with config profiles called docker, singularity, podman, shifter, charliecloud and conda which instruct the pipeline to use the named tool for software management. For example, -profile test,docker.

Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

If you are using singularity, please use the nf-core download command to download images first, before running the pipeline. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.

If you are using conda, it is highly recommended to use the NXF_CONDA_CACHEDIR or conda.cacheDir settings to store the environments in a central location for future pipeline runs.

Start running your own analysis!

bash nextflow run nf-core/variantcatalogue --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>

Documentation

More details about the pipeline can be found in the following preperint Correard et al., 2022

A bytesize talk about the varaint catalogue is available on the nf-core website

The nf-core/variantcatalogue pipeline comes with documentation about the pipeline usage, parameters and output.

Credits

nf-core/variantcatalogue was originally written by @scorreard.

We thank the following people for their extensive assistance in the development of this pipeline: @WyethWasserman @melsiddieg @brittanyhewitson

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #variantcatalogue channel (you can join with this invite).

Citations

If you use nf-core/variantcatalogue for your analysis, please cite it using the following doi: 10.1101/2022.10.03.508010

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

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: nf-core
Login: nf-core
Kind: organization
Email: core@nf-co.re

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md)

# nf-core/variantcatalogue: Citations

## [The varaint catalogue pipeline](https://www.biorxiv.org/content/10.1101/2022.10.03.508010v2)
> Correard S, Abdallah OE M, Hewitson B, Wasserman WW. The variant catalogue pipeline: A workflow to generate a background variant library from Whole Genome Sequences. bioRxiv 2022.10.03.508010; doi: https://doi.org/10.1101/2022.10.03.508010

## [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.

- [BWA-MEM](https://arxiv.org/abs/1303.3997v2)

  > Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013. doi: 10.48550/arXiv.1303.3997

- [DeepVariant](https://www.nature.com/articles/nbt.4235)

  > Poplin, R., Chang, PC., Alexander, D. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 36, 983–987 (2018). doi: 10.1038/nbt.4235.

- [EnsemblVEP](https://pubmed.ncbi.nlm.nih.gov/27268795/)

  > McLaren W, Gil L, Hunt SE, et al.: The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PubMed Central PMCID: PMC4893825.

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

- [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/)

  > McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.

- [GLnexus](https://academic.oup.com/bioinformatics/article/36/24/5582/6064144)

  > Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081

- [Hail](https://github.com/hail-is/hail)
> Hail Team. Hail 0.2. https://github.com/hail-is/hail

- [Mosdepth](https://academic.oup.com/bioinformatics/article/34/5/867/4583630)

  > Brent S Pedersen, Aaron R Quinlan, Mosdepth: quick coverage calculation for genomes and exomes, Bioinformatics, Volume 34, Issue 5, 01 March 2018, Pages 867–868. doi: 10.1093/bioinformatics/btx699. PubMed PMID: 29096012. PubMed Central PMCID: PMC6030888.

- [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)

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

- [TRIMMOMATIC](http://www.usadellab.org/cms/?page=trimmomatic)

  > Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. doi: 10.1093/bioinformatics/btu170

## 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)

- [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

Issues event: 1
Watch event: 4
Issue comment event: 5
Push event: 4
Pull request event: 9
Fork event: 1
Create event: 3

Last Year

Issues event: 1
Watch event: 4
Issue comment event: 5
Push event: 4
Pull request event: 9
Fork event: 1
Create event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 18
Total Committers: 1
Avg Commits per committer: 18.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 18
Committers: 1
Avg Commits per committer: 18.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Solenne Correard	s**d@g**m	18

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 1
Total pull requests: 9
Average time to close issues: N/A
Average time to close pull requests: about 1 month
Total issue authors: 1
Total pull request authors: 2
Average comments per issue: 0.0
Average comments per pull request: 0.44
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 3
Average time to close issues: N/A
Average time to close pull requests: about 2 months
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.67
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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lukouxinan (1)
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nf-core-bot (16)
scorreard (3)
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Top Labels

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bug (1) enhancement (1)

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Dependencies

.github/workflows/awsfulltest.yml actions

actions/upload-artifact v3 composite
nf-core/tower-action v3 composite

.github/workflows/awstest.yml actions

actions/upload-artifact v3 composite
nf-core/tower-action v3 composite

.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/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/local/bcftools/norm/meta.yml cpan

modules/local/bwa/mem/meta.yml cpan

modules/local/collecthsmetrics/meta.yml cpan

modules/local/deepvariant/meta.yml cpan

modules/local/filtermutectcalls/meta.yml cpan

modules/local/gatk4/leftalignandtrimvariants/meta.yml cpan

modules/local/gatk4/mergemutectstats/meta.yml cpan

modules/local/gatk4/printreads/meta.yml cpan

modules/local/gatk4/samtofastq/meta.yml cpan

modules/local/haplocheck/meta.yml cpan

modules/local/variantfiltration/meta.yml cpan

modules/nf-core/bcftools/annotate/meta.yml cpan

modules/nf-core/bcftools/norm/meta.yml cpan

modules/nf-core/bwa/index/meta.yml cpan

modules/nf-core/bwa/mem/meta.yml cpan

modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan

modules/nf-core/deepvariant/meta.yml cpan

modules/nf-core/ensemblvep/vep/meta.yml cpan

modules/nf-core/fastqc/meta.yml cpan

modules/nf-core/gatk4/filtermutectcalls/meta.yml cpan

modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml cpan

modules/nf-core/gatk4/markduplicates/meta.yml cpan

modules/nf-core/gatk4/mergemutectstats/meta.yml cpan

modules/nf-core/gatk4/mergevcfs/meta.yml cpan

modules/nf-core/gatk4/mutect2/meta.yml cpan

modules/nf-core/gatk4/printreads/meta.yml cpan

modules/nf-core/gatk4/samtofastq/meta.yml cpan

modules/nf-core/gatk4/variantfiltration/meta.yml cpan

modules/nf-core/glnexus/meta.yml cpan

modules/nf-core/haplocheck/meta.yml cpan

modules/nf-core/mosdepth/meta.yml cpan

modules/nf-core/multiqc/meta.yml cpan

modules/nf-core/picard/collecthsmetrics/meta.yml cpan

modules/nf-core/picard/collectwgsmetrics/meta.yml cpan

modules/nf-core/samtools/index/meta.yml cpan

modules/nf-core/tabix/tabix/meta.yml cpan

modules/nf-core/trimmomatic/meta.yml cpan

pyproject.toml pypi

variantcatalogue

Science Score: 54.0%

Keywords

Repository

Basic Info

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Metadata Files

README.md

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Quick Start

Documentation

Credits

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Citations

Owner

Citation (CITATIONS.md)

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