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rnavar

gatk4 RNA variant calling pipeline

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

Science Score: 57.0%

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 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.2%) to scientific vocabulary

Keywords

gatk4 nextflow nf-core pipeline rna rnaseq variant-calling worflow workflow

Keywords from Contributors

atac-seq chromatin-accessibiity alignment demultiplexing nanopore qc
Last synced: 6 months ago · JSON representation ·

Repository

gatk4 RNA variant calling pipeline

Basic Info
  • Host: GitHub
  • Owner: nf-core
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage: https://nf-co.re/rnavar
  • Size: 4.21 MB
Statistics
  • Stars: 52
  • Watchers: 126
  • Forks: 41
  • Open Issues: 17
  • Releases: 4
Topics
gatk4 nextflow nf-core pipeline rna rnaseq variant-calling worflow workflow
Created almost 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/rnavar

GitHub Actions CI Status GitHub Actions Linting Status AWS CI Cite with Zenodo nf-test

Nextflow nf-core template version run with conda run with docker run with singularity Launch on Seqera Platform

Get help on Slack Follow on Bluesky Follow on Mastodon Watch on YouTube

Introduction

nf-core/rnavar is a bioinformatics pipeline for RNA variant calling analysis following GATK4 best practices.

Pipeline summary

  1. Merge re-sequenced FastQ files (cat)
  2. Read QC (FastQC)
  3. (Optionally) Extract UMIs from FASTQ reads (UMI-tools)
  4. (Optionally) HLATyping from FASTQ reads (Seq2HLA)
  5. Align reads to reference genome (STAR)
  6. Sort and index alignments (SAMtools)
  7. Duplicate read marking (Picard MarkDuplicates)
  8. Scatter one interval-list into many interval-files (GATK4 IntervalListTools)
  9. Splits reads that contain Ns in their cigar string (GATK4 SplitNCigarReads)
  10. Estimate and correct systematic bias using base quality score recalibration (GATK4 BaseRecalibrator, GATK4 ApplyBQSR)
  11. Convert a BED file to a Picard Interval List (GATK4 BedToIntervalList)
  12. Call SNPs and indels (GATK4 HaplotypeCaller)
  13. Merge multiple VCF files into one VCF (GATK4 MergeVCFs)
  14. Index the VCF (Tabix)
  15. Filter variant calls based on certain criteria (GATK4 VariantFiltration)
  16. Annotate variants (BCFtools Annotate, snpEff, Ensembl VEP)
  17. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks (MultiQC, R)

Summary of tools and version used in the pipeline

| Tool | Version | | ----------- | ------- | | BCFtools | 1.21 | | BEDtools | 2.31.1 | | Ensembl VEP | 114.2 | | FastQC | 0.12.1 | | GATK | 4.6.1.0 | | mosdepth | 0.3.10 | | MultiQC | 1.29 | | Picard | 3.3.0 | | Samtools | 1.21 | | Seq2HLA | 2.3 | | SnpEff | 5.1 | | STAR | 2.7.11b | | Tabix | 1.20 | | UMI-tools | 1.1.5 |

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,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

console nextflow run nf-core/rnavar -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --outdir <OUTDIR> --genome GRCh38

[!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.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

rnavar was originally written by Praveen Raj and Maxime U Garcia at The Swedish Childhood Tumor Biobank (Barntumörbanken), Karolinska Institutet. Nicolas Vannieuwkerke at CMGG later joined and helped with further development (v 1.1.0 and forward).

Maintenance is now lead by Maxime U Garcia (now at Seqera)

Main developers:

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.

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

Citations

If you use nf-core/rnavar for your analysis, please cite it using the following doi: 10.5281/zenodo.6669636

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

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

Citation (CITATIONS.md) 

# nf-core/rnavar: 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.

- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)

  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PMID: 20110278; PMCID: PMC2832824.

- [cat](https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html#cat-invocation)

- [coreutils](https://www.gnu.org/software/coreutils/)

- [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/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [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.

- [gawk](https://www.gnu.org/software/gawk/)

- [GffRead](https://f1000research.com/articles/9-304/v1)

  > Pertea G and Pertea M. GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved]. F1000Research 2020, 9:304 (https://doi.org/10.12688/f1000research.23297.1)

- [grep](https://www.gnu.org/software/grep/)

- [gzip](https://www.gnu.org/software/gzip/)

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

  > “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute

- [R](https://www.R-project.org/)

  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

- [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.

- [sed](https://www.gnu.org/software/sed/)

- [snpEff](https://pubmed.ncbi.nlm.nih.gov/22728672/)

  > Cingolani P, Platts A, Wang le L, et al.: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). Apr-Jun 2012;6(2):80-92. doi: 10.4161/fly.19695. PubMed PMID: 22728672; PubMed Central PMCID: PMC3679285.

- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)

  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

- [Tabix](https://pubmed.ncbi.nlm.nih.gov/21208982/)

  > Heng Li, 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.

- [tar](https://www.gnu.org/software/tar/)

- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)

  > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PMID: 28100584; PMCID: PMC5340976.

- [VEP](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.

## 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: 12
  • Release event: 2
  • Issues event: 55
  • Watch event: 12
  • Delete event: 13
  • Issue comment event: 134
  • Push event: 67
  • Pull request review comment event: 89
  • Pull request review event: 133
  • Pull request event: 91
  • Fork event: 10
Last Year
  • Create event: 12
  • Release event: 2
  • Issues event: 55
  • Watch event: 12
  • Delete event: 13
  • Issue comment event: 134
  • Push event: 67
  • Pull request review comment event: 89
  • Pull request review event: 133
  • Pull request event: 91
  • Fork event: 10

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 237
  • Total Committers: 7
  • Avg Commits per committer: 33.857
  • Development Distribution Score (DDS): 0.194
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Praveen p****6@g****m 191
MaxUlysse m****a@g****m 20
praveenraj2018 4****8@u****m 13
nf-core-bot c****e@n****e 7
m3hdad m****i@g****m 3
Maxime U. Garcia m****a@s****e 2
kevinmenden k****n@t****e 1
Committer Domains (Top 20 + Academic)
t-online.de: 1 scilifelab.se: 1 nf-co.re: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 63
  • Total pull requests: 119
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 12 days
  • Total issue authors: 43
  • Total pull request authors: 10
  • Average comments per issue: 2.37
  • Average comments per pull request: 1.58
  • Merged pull requests: 83
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 18
  • Pull requests: 48
  • Average time to close issues: 13 days
  • Average time to close pull requests: 5 days
  • Issue authors: 15
  • Pull request authors: 5
  • Average comments per issue: 2.39
  • Average comments per pull request: 1.23
  • Merged pull requests: 36
  • Bot issues: 0
  • Bot pull requests: 0
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Issue Authors
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Pull Request Authors
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Dependencies

.github/workflows/awsfulltest.yml actions
  • nf-core/tower-action v3 composite
.github/workflows/awstest.yml actions
  • nf-core/tower-action v3 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v2 composite
.github/workflows/linting.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v2 composite
  • actions/setup-python v3 composite
  • actions/upload-artifact v2 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/modules/ensemblvep/Dockerfile docker
  • nfcore/base 1.14 build
modules/nf-core/modules/snpeff/Dockerfile docker
  • nfcore/base 1.14 build
modules/nf-core/modules/cat/fastq/meta.yml cpan
modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/modules/ensemblvep/meta.yml cpan
modules/nf-core/modules/fastqc/meta.yml cpan
modules/nf-core/modules/gatk4/applybqsr/meta.yml cpan
modules/nf-core/modules/gatk4/baserecalibrator/meta.yml cpan
modules/nf-core/modules/gatk4/bedtointervallist/meta.yml cpan
modules/nf-core/modules/gatk4/createsequencedictionary/meta.yml cpan
modules/nf-core/modules/gatk4/haplotypecaller/meta.yml cpan
modules/nf-core/modules/gatk4/indexfeaturefile/meta.yml cpan
modules/nf-core/modules/gatk4/intervallisttools/meta.yml cpan
modules/nf-core/modules/gatk4/markduplicates/meta.yml cpan
modules/nf-core/modules/gatk4/mergevcfs/meta.yml cpan
modules/nf-core/modules/gatk4/splitncigarreads/meta.yml cpan
modules/nf-core/modules/gatk4/variantfiltration/meta.yml cpan
modules/nf-core/modules/gffread/meta.yml cpan
modules/nf-core/modules/gunzip/meta.yml cpan
modules/nf-core/modules/multiqc/meta.yml cpan
modules/nf-core/modules/samtools/faidx/meta.yml cpan
modules/nf-core/modules/samtools/flagstat/meta.yml cpan
modules/nf-core/modules/samtools/idxstats/meta.yml cpan
modules/nf-core/modules/samtools/index/meta.yml cpan
modules/nf-core/modules/samtools/merge/meta.yml cpan
modules/nf-core/modules/samtools/sort/meta.yml cpan
modules/nf-core/modules/samtools/stats/meta.yml cpan
modules/nf-core/modules/snpeff/meta.yml cpan
modules/nf-core/modules/star/align/meta.yml cpan
modules/nf-core/modules/star/genomegenerate/meta.yml cpan
modules/nf-core/modules/tabix/bgziptabix/meta.yml cpan
modules/nf-core/modules/tabix/tabix/meta.yml cpan
modules/nf-core/modules/untar/meta.yml cpan
modules/nf-core/modules/ensemblvep/environment.yml pypi
modules/nf-core/modules/snpeff/environment.yml pypi