How do I install the Vcfutils Pl skill?

Run npx skillmds add vimalinx/vcfutils-pl 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.

What does the Vcfutils Pl skill do?

Use when working with VCF file utilities from the bcftools bioconda package. It is listed under Coding & Dev Tools on SkillMD.

Is Vcfutils Pl safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Vcfutils Pl?

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 Vcfutils Pl free to use?

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

Who published Vcfutils Pl?

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

Vcfutils Pl by vimalinx — Agent Skill

Name: Vcfutils Pl
Rating: 4.5 (4 reviews)
Author: vimalinx

File contents

vcfutils-pl

Quick Start

Command: vcfutils.pl <command> [arguments]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcfutils.pl
Reference: See references/help.md for detailed usage

When To Use This Tool

Run legacy VCF helper subcommands bundled with the bcftools toolchain.
Subset samples, list sample names, or fill AC/AN counts in VCF records.
Compute quick quality statistics or apply the legacy varFilter.
Convert all-site VCF output into consensus FASTQ with vcf2fq.

Common Patterns

# 1) List sample names in a VCF
vcfutils.pl \
  listsam \
  cohort.vcf

# 2) Fill AC/AN fields from genotypes
vcfutils.pl \
  fillac \
  cohort.vcf \
  > cohort.with-ac.vcf

# 3) Apply the legacy short-variant filter helper
vcfutils.pl \
  varFilter \
  cohort.vcf \
  > cohort.filtered.vcf

# 4) Build a consensus FASTQ from an all-site VCF
vcfutils.pl \
  vcf2fq \
  all-sites.vcf \
  > consensus.fq

Recommended Workflow

Start by choosing the subcommand that matches the task, because vcfutils.pl is a command multiplexer rather than a single-purpose tool.
Validate whether the chosen subcommand expects ordinary VCF input, an all-site VCF, a .fai, or bcftools-specific annotations.
Run the subcommand and redirect output into a new file, because most modes write transformed text to stdout.
Re-validate the resulting VCF/FASTQ before plugging it into downstream analysis.

Guardrails

The first argument must be a subcommand such as listsam, fillac, qstats, varFilter, or vcf2fq; -h, --help, and --version are not valid top-level help flags.
fillac expects the GT field to be present and to appear first in the FORMAT column.
vcf2fq is intended for all-site, position-sorted VCF input and will complain about unsorted data.
varFilter and some related commands rely on annotations produced by the SAMtools/BCFtools legacy calling pipeline.

---name: vcfutils-pldescription: Use when working with VCF file utilities from the bcftools bioconda package.--- # vcfutils-pl ## Quick Start - **Command**: `vcfutils.pl <command> [arguments]` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/vcfutils.pl` - **Reference**: See [references/help.md](references/help.md) for detailed usage ## When To Use This Tool - Run legacy VCF helper subcommands bundled with the `bcftools` toolchain. - Subset samples, list sample names, or fill `AC/AN` counts in VCF records. - Compute quick quality statistics or apply the legacy `varFilter`. - Convert all-site VCF output into consensus FASTQ with `vcf2fq`. ## Common Patterns ```bash # 1) List sample names in a VCF vcfutils.pl \ listsam \ cohort.vcf ``` ```bash # 2) Fill AC/AN fields from genotypes vcfutils.pl \ fillac \ cohort.vcf \ > cohort.with-ac.vcf ``` ```bash # 3) Apply the legacy short-variant filter helper vcfutils.pl \ varFilter \ cohort.vcf \ > cohort.filtered.vcf ``` ```bash # 4) Build a consensus FASTQ from an all-site VCF vcfutils.pl \ vcf2fq \ all-sites.vcf \ > consensus.fq ``` ## Recommended Workflow 1. Start by choosing the subcommand that matches the task, because `vcfutils.pl` is a command multiplexer rather than a single-purpose tool. 2. Validate whether the chosen subcommand expects ordinary VCF input, an all-site VCF, a `.fai`, or bcftools-specific annotations. 3. Run the subcommand and redirect output into a new file, because most modes write transformed text to stdout. 4. Re-validate the resulting VCF/FASTQ before plugging it into downstream analysis. ## Guardrails - The first argument must be a subcommand such as `listsam`, `fillac`, `qstats`, `varFilter`, or `vcf2fq`; `-h`, `--help`, and `--version` are not valid top-level help flags. - `fillac` expects the `GT` field to be present and to appear first in the FORMAT column. - `vcf2fq` is intended for all-site, position-sorted VCF input and will complain about unsorted data. - `varFilter` and some related commands rely on annotations produced by the SAMtools/BCFtools legacy calling pipeline.

Frequently asked questions