IGVreport-nf: Efficient Generation of Interactive IGV HTML Reports for Genomic Regions of Interest in Human Genome (hg38)

public 1yr ago Version: Version 1 0 bookmarks

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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

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.

Code Snippets

"""
bcftools view ${params.vcf} \
  -r ${params.chr}:${params.start}-${params.stop} \
  -Oz -o ${params.sample}_${params.chr}_${params.start}-${params.stop}.vcf.gz
"""

NextFlow BCFtools From line 17 of modules/Extract.nf

"""
bcftools index ${params.sample}_${params.chr}_${params.start}-${params.stop}.vcf.gz
"""

NextFlow BCFtools From line 17 of modules/Index.nf

"""
create_report \
  ${params.sample}_${params.chr}_${params.start}-${params.stop}.vcf.gz \
  --genome hg38 \
  --info-columns SVTYPE SVLEN CHR2 \
  --flanking 10000 \
  --tracks ${params.sample}_${params.chr}_${params.start}-${params.stop}.vcf.gz ${params.bam} \
  --output ${params.sample}_${params.chr}_${params.start}-${params.stop}.html
"""