How do I install the Vcftools skill?

Run npx skillmds add vimalinx/vcftools 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 Vcftools 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 Vcftools?

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 Vcftools free to use?

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

Who published Vcftools?

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

Vcftools by vimalinx — Agent Skill

Name: Vcftools
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

vcftools

Quick Start

Command: vcftools
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcftools
Version: 0.1.17
Full reference: See references/help.md and the installed man page under /home/vimalinx/miniforge3/envs/bio/share/man/man1/vcftools.1

When To Use This Tool

Filter VCF or BCF files by site, variant type, allele frequency, or missingness.
Export summary statistics such as allele frequency, Hardy-Weinberg tests, or site depth.
Recode filtered VCFs for downstream tools.
Prefer vcftools for classic population-genetics style filtering and quick summaries.

Common Patterns

# 1) SNP-only filtered VCF
vcftools \
  --gzvcf cohort.vcf.gz \
  --remove-indels \
  --recode --recode-INFO-all \
  --out cohort.snps_only

# 2) Common-variant, low-missingness filter
vcftools \
  --gzvcf cohort.vcf.gz \
  --maf 0.05 \
  --max-missing 0.9 \
  --recode --recode-INFO-all \
  --out cohort.filtered

# 3) Allele-frequency report for one chromosome
vcftools \
  --gzvcf cohort.vcf.gz \
  --freq \
  --chr 1 \
  --out chr1.freq

# 4) Site mean depth summary
vcftools \
  --gzvcf cohort.vcf.gz \
  --site-mean-depth \
  --out cohort.depth

Recommended Workflow

Pick the correct input mode first: --vcf, --gzvcf, or --bcf.
Separate filtering passes from statistics passes so outputs stay interpretable.
When writing a new VCF, use --recode and usually --recode-INFO-all.
Keep the filtering thresholds documented, because small MAF or missingness changes can materially alter results.

Guardrails

If --out is omitted, files default to the out.* prefix in the current directory.
--recode writes a new VCF; without it many filtering commands only emit summary files.
--max-missing 1.0 keeps only sites with no missing genotypes, which is often much harsher than intended.
Distinguish site filters from genotype-aware downstream interpretation; filtering can strongly bias frequency-based summaries.

---name: vcftoolsdescription: Use when working with Variant Call Format (VCF) files and need to filter, summarize, or manipulate variant data.--- # vcftools ## Quick Start - **Command:** `vcftools` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/vcftools` - **Version:** 0.1.17 - **Full reference:** See [references/help.md](references/help.md) and the installed man page under `/home/vimalinx/miniforge3/envs/bio/share/man/man1/vcftools.1` ## When To Use This Tool - Filter VCF or BCF files by site, variant type, allele frequency, or missingness. - Export summary statistics such as allele frequency, Hardy-Weinberg tests, or site depth. - Recode filtered VCFs for downstream tools. - Prefer `vcftools` for classic population-genetics style filtering and quick summaries. ## Common Patterns ```bash # 1) SNP-only filtered VCF vcftools \ --gzvcf cohort.vcf.gz \ --remove-indels \ --recode --recode-INFO-all \ --out cohort.snps_only ``` ```bash # 2) Common-variant, low-missingness filter vcftools \ --gzvcf cohort.vcf.gz \ --maf 0.05 \ --max-missing 0.9 \ --recode --recode-INFO-all \ --out cohort.filtered ``` ```bash # 3) Allele-frequency report for one chromosome vcftools \ --gzvcf cohort.vcf.gz \ --freq \ --chr 1 \ --out chr1.freq ``` ```bash # 4) Site mean depth summary vcftools \ --gzvcf cohort.vcf.gz \ --site-mean-depth \ --out cohort.depth ``` ## Recommended Workflow 1. Pick the correct input mode first: `--vcf`, `--gzvcf`, or `--bcf`. 2. Separate filtering passes from statistics passes so outputs stay interpretable. 3. When writing a new VCF, use `--recode` and usually `--recode-INFO-all`. 4. Keep the filtering thresholds documented, because small MAF or missingness changes can materially alter results. ## Guardrails - If `--out` is omitted, files default to the `out.*` prefix in the current directory. - `--recode` writes a new VCF; without it many filtering commands only emit summary files. - `--max-missing 1.0` keeps only sites with no missing genotypes, which is often much harsher than intended. - Distinguish site filters from genotype-aware downstream interpretation; filtering can strongly bias frequency-based summaries.

Frequently asked questions