| name | roh-viz |
| description | Use when turning `bcftools roh` output plus a VCF/BCF into an interactive HTML visualization of ROH segments and homozygosity rates. |
| disable-model-invocation | true |
| user-invocable | true |
roh-viz
Perl HTML report generator for ROH review. It parses RG segments from bcftools roh output, queries alt-genotype calls from the supplied VCF/BCF with bcftools query, then renders an HTML/JavaScript report with optional embedded D3/Pako assets.
Quick Start
- Command:
roh-viz -i roh.txt -v cohort.bcf -o output.html
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/roh-viz
- Required companions:
bcftools, bash, zless
When To Use This Tool
- Reviewing runs of homozygosity from
bcftools roh in a browser instead of raw text
- Combining ROH segments with homozygosity-rate traces derived from the source VCF/BCF
- Filtering the visualization by samples, regions, or minimum ROH length
- Generating a self-contained offline HTML report with embedded JavaScript assets
Common Patterns
bcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt cohort.bcf
roh-viz -i roh.txt -v cohort.bcf -o roh.html
roh-viz -i roh.txt -v cohort.bcf -e 1 -o roh_offline.html
roh-viz -i roh.txt -v cohort.bcf -s sample1,sample2 -r chr1,chr2 -l 500000 -o subset.html
Recommended Workflow
- Generate
bcftools roh output first, then keep the original VCF/BCF available for genotype-rate calculation.
- Feed the ROH text through
-i and the variant file through -v.
- Tune
-l, -s, and -r to reduce clutter before sharing the report.
- Use
-e 1 whenever the final HTML must work without internet access.
Guardrails
- The real ROH-input flag is
-i, not -r. Source inspection shows -r means genomic regions, but the built-in error message and example text incorrectly say Missing the -r option / roh-viz -r roh.txt ....
- Both
-i and -v are required by the parser.
- The script shells out to
bcftools query and zless, so those tools must be available on PATH.
- Only
RG lines from the ROH file are plotted as ROH segments; other record types are ignored.
- If
-o is omitted, the script writes HTML to stdout.
- By default it links D3/Pako from remote URLs; use
-e 1 to embed those assets for offline viewing.
