How do I install the Vcf Convert skill?

Run npx skillmds add vimalinx/vcf-convert 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 Vcf Convert 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 Vcf Convert?

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 Vcf Convert free to use?

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

Who published Vcf Convert?

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

Vcf Convert by vimalinx — Agent Skill

Name: Vcf Convert
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

vcf-convert

Quick Start

Command: vcf-convert -v <4.0|4.1|4.2> [options] < in.vcf > out.vcf
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert
Fallback launcher in this workspace: /home/vimalinx/miniforge3/envs/bio/bin/perl /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert
Full reference: See references/help.md

When To Use This Tool

Convert a VCF stream between versions 4.0, 4.1, and 4.2 for downstream compatibility.
Upgrade older VCFs before handing them to newer tooling.
Normalize indel representation during version conversion when you can provide the reference FASTA.
Keep using it only if you already depend on the vcftools Perl helpers; for fresh pipelines, prefer modern bcftools-based normalization when possible.

Common Patterns

# 1) Upgrade an older SNP-only VCF to 4.2
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \
  -v 4.2 \
  < input.vcf > output.vcf

# 2) Convert an indel-containing VCF with a faidx-indexed reference
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \
  -v 4.2 \
  -r ref.fa \
  < input.vcf > output.vcf

# 3) Downgrade cautiously for an older consumer
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \
  -v 4.1 \
  < input.vcf > output.vcf

Recommended Workflow

Confirm which VCF version the downstream tool actually requires before converting anything.
Treat the input as a stream: feed it on stdin and capture the converted VCF from stdout.
Provide -r ref.fa whenever non-SNP variants are present so indel REF / ALT rewriting is well-defined.
Validate the output with a downstream parser or vcf-validator before swapping it into a pipeline.

Guardrails

In this shell, direct invocation may fail with Can't locate Vcf.pm; activate the bio environment first or call the script through /home/vimalinx/miniforge3/envs/bio/bin/perl.
The -v/--version option sets the target VCF format version; it is not a program-version flag.
Downgrading VCF versions is explicitly marked upstream as experimental.
Indel conversion needs a samtools-faidx indexed reference FASTA via -r.
This tool reads from stdin and writes to stdout; it does not edit files in place.

---name: vcf-convertdescription: Use when converting VCF files between format versions (4.0, 4.1, 4.2) for compatibility with downstream bioinformatics tools.--- # vcf-convert ## Quick Start - **Command:** `vcf-convert -v <4.0|4.1|4.2> [options] < in.vcf > out.vcf` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/vcf-convert` - **Fallback launcher in this workspace:** `/home/vimalinx/miniforge3/envs/bio/bin/perl /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert` - **Full reference:** See `references/help.md` ## When To Use This Tool - Convert a VCF stream between versions 4.0, 4.1, and 4.2 for downstream compatibility. - Upgrade older VCFs before handing them to newer tooling. - Normalize indel representation during version conversion when you can provide the reference FASTA. - Keep using it only if you already depend on the vcftools Perl helpers; for fresh pipelines, prefer modern `bcftools`-based normalization when possible. ## Common Patterns ```bash # 1) Upgrade an older SNP-only VCF to 4.2 /home/vimalinx/miniforge3/envs/bio/bin/perl \ /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \ -v 4.2 \ < input.vcf > output.vcf ``` ```bash # 2) Convert an indel-containing VCF with a faidx-indexed reference /home/vimalinx/miniforge3/envs/bio/bin/perl \ /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \ -v 4.2 \ -r ref.fa \ < input.vcf > output.vcf ``` ```bash # 3) Downgrade cautiously for an older consumer /home/vimalinx/miniforge3/envs/bio/bin/perl \ /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \ -v 4.1 \ < input.vcf > output.vcf ``` ## Recommended Workflow 1. Confirm which VCF version the downstream tool actually requires before converting anything. 2. Treat the input as a stream: feed it on stdin and capture the converted VCF from stdout. 3. Provide `-r ref.fa` whenever non-SNP variants are present so indel REF / ALT rewriting is well-defined. 4. Validate the output with a downstream parser or `vcf-validator` before swapping it into a pipeline. ## Guardrails - In this shell, direct invocation may fail with `Can't locate Vcf.pm`; activate the bio environment first or call the script through `/home/vimalinx/miniforge3/envs/bio/bin/perl`. - The `-v/--version` option sets the target VCF format version; it is not a program-version flag. - Downgrading VCF versions is explicitly marked upstream as experimental. - Indel conversion needs a samtools-faidx indexed reference FASTA via `-r`. - This tool reads from stdin and writes to stdout; it does not edit files in place.

Frequently asked questions