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:
- The provided VCF file is subset to a region of interest using Bcftools view
- The Subset VCF file is then indexed using Bcftools index
- 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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Created: 21st Mar 2023 at 05:17
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