How do I install the Plot Vcfstats skill?

Run npx skillmds add vimalinx/plot-vcfstats 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.

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Is Plot Vcfstats free to use?

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Who published Plot Vcfstats?

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

Plot Vcfstats by vimalinx — Agent Skill

Name: Plot Vcfstats
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

plot-vcfstats

Perl plotting helper for bcftools stats. It parses one or more .vchk files, writes an output directory with plot.py, PNG images, and intermediate .dat tables, and optionally tries to render a PDF report.

Quick Start

Command: plot-vcfstats -p <outdir> <file.vchk>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/plot-vcfstats
Upstream producer: bcftools stats

When To Use This Tool

Plotting output from bcftools stats into PDF visualizations
Merging multiple vcfstats files into a single stream
Generating per-sample PNG QC panels without writing custom plotting code
Editing the auto-generated plot.py if the default aesthetics are not enough

Common Patterns

# 1) Generate stats and plot them
bcftools stats -s - calls.vcf.gz > calls.vchk
plot-vcfstats -p outdir calls.vchk

# 2) Skip PDF generation when LaTeX is unavailable
plot-vcfstats -P -p outdir calls.vchk

# 3) Merge multiple stats files instead of plotting
plot-vcfstats -m sample1.vchk sample2.vchk > merged.vchk

Recommended Workflow

Generate a real .vchk file with bcftools stats; this tool validates the file header and will reject hand-rolled approximations.
Plot into a dedicated output directory via -p.
If you only need PNG/data outputs, add -P to bypass PDF rendering.
Customize outdir/plot.py and rerun it manually if the stock plots need layout or style changes.

Guardrails

--help works, but --version is not a real metadata path; it is treated as an unknown parameter.
A fake .vchk file failed with Sanity check failed: was this file generated by bcftools stats?, so input validation is strict.
In live testing, a real one-record .vchk plus -P successfully generated files such as plot.py, plot-vcfstats.log, snps_by_sample.0.png, and several *.dat tables.
Without -P, the same run failed at the PDF stage because neither pdflatex nor tectonic was installed.
-m/--merge skips plotting and writes merged stats to stdout instead.

---name: plot-vcfstatsdescription: Use when converting `bcftools stats` output into variant-QC plots, per-sample PNG panels, and optional PDF summaries.--- # plot-vcfstats Perl plotting helper for `bcftools stats`. It parses one or more `.vchk` files, writes an output directory with `plot.py`, PNG images, and intermediate `.dat` tables, and optionally tries to render a PDF report. ## Quick Start - **Command:** `plot-vcfstats -p <outdir> <file.vchk>` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/plot-vcfstats` - **Upstream producer:** `bcftools stats` ## When To Use This Tool - Plotting output from `bcftools stats` into PDF visualizations - Merging multiple vcfstats files into a single stream - Generating per-sample PNG QC panels without writing custom plotting code - Editing the auto-generated `plot.py` if the default aesthetics are not enough ## Common Patterns ```bash # 1) Generate stats and plot them bcftools stats -s - calls.vcf.gz > calls.vchk plot-vcfstats -p outdir calls.vchk ``` ```bash # 2) Skip PDF generation when LaTeX is unavailable plot-vcfstats -P -p outdir calls.vchk ``` ```bash # 3) Merge multiple stats files instead of plotting plot-vcfstats -m sample1.vchk sample2.vchk > merged.vchk ``` ## Recommended Workflow 1. Generate a real `.vchk` file with `bcftools stats`; this tool validates the file header and will reject hand-rolled approximations. 2. Plot into a dedicated output directory via `-p`. 3. If you only need PNG/data outputs, add `-P` to bypass PDF rendering. 4. Customize `outdir/plot.py` and rerun it manually if the stock plots need layout or style changes. ## Guardrails - `--help` works, but `--version` is not a real metadata path; it is treated as an unknown parameter. - A fake `.vchk` file failed with `Sanity check failed: was this file generated by bcftools stats?`, so input validation is strict. - In live testing, a real one-record `.vchk` plus `-P` successfully generated files such as `plot.py`, `plot-vcfstats.log`, `snps_by_sample.0.png`, and several `*.dat` tables. - Without `-P`, the same run failed at the PDF stage because neither `pdflatex` nor `tectonic` was installed. - `-m/--merge` skips plotting and writes merged stats to stdout instead.

Frequently asked questions