IGVreport-nf
Version 1

Workflow Type: Nextflow
Work-in-progress

IGVreport-nf

Description

Quickly generate IGV .html reports for a genomic region of interest in the human genome (hg38). Bcftools is used to subset a VCF to a region of interest, the subset VCF is then passed to IGV-reports, which generates a report consisting of a table of genomic sites or regions and associated IGV views for each site. The reports can be opened by any web browser as a static page.

Diagram

graph LR;
    VCF-->|bcftools view|SubsetVCF;
    SubsetVCF-->|IGVtools|HTMLreport;
    AlignmentBAM-->|IGVtools|HTMLreport;

User guide

This workflow uses containers for all steps and can run using Singularity or Docker. It requires Nextflow and either Singularity or Docker be installed. For instructions on installing Nextflow, see their documentation.

This workflow currently only generates reports for the human reference genome assembly, Hg38.

The workflow runs three processes:

  1. The provided VCF file is subset to a region of interest using Bcftools view
  2. The Subset VCF file is then indexed using Bcftools index
  3. The subset VCF and provided Bam file are used to generate the html report for the region of interest.

To start clone this repository:

git clone https://github.com/Sydney-Informatics-Hub/IGVreport-nf.git

From the IGVreport-nf directory, run the pipeline:

nextflow run main.nf --sample  \
    --bam  \
    --vcf  \
    --chr  --start  --stop      

This will create a report in a directory titled ./Report. You can rename this directory at runtime using the flag --outDir. All runtime summary reports will be available in the ./runInfo directory.

Workflow summaries

Metadata

metadata field workflow_name / workflow_version
Version 1.0
Maturity under development
Creators Georgie Samaha
Source NA
License GPL-3.0 license
Workflow manager NextFlow
Container None
Install method NA
GitHub github.com/Sydney-Informatics-Hub/IGVreport-nf
bio.tools NA
BioContainers NA
bioconda NA

Component tools

  • nextflow>=20.07.1
  • singularity or docker
  • bcftools/1.16
  • igv-reports/1.6.1

Required (minimum) inputs/parameters

  • An indexed alignment file in Bam format
  • A gzipped and indexed vcf file

Additional notes

Help/FAQ/troubleshooting

Acknowledgements/citations/credits

This workflow was developed by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney and the Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia.

Version History

main @ 47b1b65 (earliest) Created 21st Mar 2023 at 05:17 by Georgina Samaha

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