How do I install the Roh Viz skill?

Run npx skillmds@latest add vimalinx/roh-viz in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Roh Viz safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Roh Viz?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Roh Viz free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Roh Viz?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Roh Viz by vimalinx — Agent Skill

Name: Roh Viz
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

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

# Basic ROH visualization
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

# Embed JavaScript for offline viewing
roh-viz -i roh.txt -v cohort.bcf -e 1 -o roh_offline.html

# Restrict to selected samples and regions
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.

---name: roh-vizdescription: Use when turning `bcftools roh` output plus a VCF/BCF into an interactive HTML visualization of ROH segments and homozygosity rates.---# roh-vizPerl 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```bash# Basic ROH visualizationbcftools roh --AF-dflt 0.5 -G 30 -Or -o roh.txt cohort.bcfroh-viz -i roh.txt -v cohort.bcf -o roh.html``````bash# Embed JavaScript for offline viewingroh-viz -i roh.txt -v cohort.bcf -e 1 -o roh_offline.html``````bash# Restrict to selected samples and regionsroh-viz -i roh.txt -v cohort.bcf -s sample1,sample2 -r chr1,chr2 -l 500000 -o subset.html```## Recommended Workflow1. Generate `bcftools roh` output first, then keep the original VCF/BCF available for genotype-rate calculation.2. Feed the ROH text through `-i` and the variant file through `-v`.3. Tune `-l`, `-s`, and `-r` to reduce clutter before sharing the report.4. 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.

Frequently asked questions

Roh Viz