How do I install the Vrfs Variances skill?

Run npx skillmds add vimalinx/vrfs-variances 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 Vrfs Variances free to use?

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

Who published Vrfs Variances?

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

Vrfs Variances by vimalinx — Agent Skill

Name: Vrfs Variances
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

vrfs-variances

Perl parser for bcftools/vrfs SITE lines. It sorts candidate loci by their trailing distribution vector, keeps either a fraction or an absolute number of sites, and then emits one of three things: a default mixed summary, a site list, or a pure variance vector suitable for feeding back into bcftools +vrfs -r.

Quick Start

Command: bcftools +vrfs ... | vrfs-variances -n 0.2
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vrfs-variances
Input contract: reads SITE\t... lines from stdin

When To Use This Tool

Selecting a subset of bcftools +vrfs sites by fraction or absolute count
Computing the VAR2 vector expected by downstream bcftools +vrfs -r workflows
Listing which SITE lines survived the ranking step
Adding reproducible random perturbation to the site distributions before variance calculation

Common Patterns

# Default summary from 20% of sites
bcftools +vrfs ... | vrfs-variances -n 0.2

# Emit only the variance vector for bcftools +vrfs -r
bcftools +vrfs ... | vrfs-variances -n 100 -v > var2.txt

# List the selected sites instead of summary numbers
bcftools +vrfs ... | vrfs-variances -n 100 -s > selected_sites.txt

Recommended Workflow

Feed genuine SITE records from bcftools +vrfs into stdin.
Decide whether -n should be a fraction (<=1) or an absolute count (>1).
Use the default mode for quick diagnostics, -s for site inspection, or -v for downstream machine-readable variance values.
Add -r <seed> only when you deliberately want stochastic perturbation and reproducibility.

Guardrails

This tool is stdin-driven. If stdin is a TTY and you give no arguments, it prints the help message and exits.
Only lines beginning with SITE are parsed; everything else is ignored.
-n <= 1 is treated as a fraction of the sorted sites, while -n > 1 is treated as an absolute count.
Default mode writes MEAN and VAR2 summaries to stderr but also prints the final selected SITE line to stdout, so capture streams intentionally.
Local testing showed -s can duplicate the final selected site because the current code prints it once from the list-sites path and once again when the selection limit is reached.
-v prints only the numeric variance vector, one value per line.

---name: vrfs-variancesdescription: Use when summarizing `bcftools +vrfs`/`vrfs` `SITE` output into selected sites or variance vectors from a subset of loci.--- # vrfs-variances Perl parser for `bcftools/vrfs` `SITE` lines. It sorts candidate loci by their trailing distribution vector, keeps either a fraction or an absolute number of sites, and then emits one of three things: a default mixed summary, a site list, or a pure variance vector suitable for feeding back into `bcftools +vrfs -r`. ## Quick Start - **Command:** `bcftools +vrfs ... | vrfs-variances -n 0.2` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/vrfs-variances` - **Input contract:** reads `SITE\t...` lines from stdin ## When To Use This Tool - Selecting a subset of `bcftools +vrfs` sites by fraction or absolute count - Computing the `VAR2` vector expected by downstream `bcftools +vrfs -r` workflows - Listing which `SITE` lines survived the ranking step - Adding reproducible random perturbation to the site distributions before variance calculation ## Common Patterns ```bash # Default summary from 20% of sites bcftools +vrfs ... | vrfs-variances -n 0.2 ``` ```bash # Emit only the variance vector for bcftools +vrfs -r bcftools +vrfs ... | vrfs-variances -n 100 -v > var2.txt ``` ```bash # List the selected sites instead of summary numbers bcftools +vrfs ... | vrfs-variances -n 100 -s > selected_sites.txt ``` ## Recommended Workflow 1. Feed genuine `SITE` records from `bcftools +vrfs` into stdin. 2. Decide whether `-n` should be a fraction (`<=1`) or an absolute count (`>1`). 3. Use the default mode for quick diagnostics, `-s` for site inspection, or `-v` for downstream machine-readable variance values. 4. Add `-r <seed>` only when you deliberately want stochastic perturbation and reproducibility. ## Guardrails - This tool is stdin-driven. If stdin is a TTY and you give no arguments, it prints the help message and exits. - Only lines beginning with `SITE` are parsed; everything else is ignored. - `-n <= 1` is treated as a fraction of the sorted sites, while `-n > 1` is treated as an absolute count. - Default mode writes `MEAN` and `VAR2` summaries to stderr but also prints the final selected `SITE` line to stdout, so capture streams intentionally. - Local testing showed `-s` can duplicate the final selected site because the current code prints it once from the list-sites path and once again when the selection limit is reached. - `-v` prints only the numeric variance vector, one value per line.

Frequently asked questions