vcf-stats

name	vcf-stats
description	Use when computing statistics on VCF files, filtering variant data by quality or fields, or generating summary reports from gzipped VCF inputs.
disable-model-invocation	true
user-invocable	true

vcf-stats

Quick Start

• Command: vcf-stats [OPTIONS] file.vcf.gz
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-stats
• Full reference: See references/help.md

When To Use This Tool

• Generate summary statistics and sample-aware reports from a gzipped VCF.
• Slice statistics by FILTER, QUAL, INFO, FORMAT, or sample-specific fields.
• Produce reusable dump files or prefixed output directories from vcftools-style stats runs.
• Use it mainly when you are already in a vcftools workflow; for broader modern VCF reporting, bcftools stats is often a better default.

Common Patterns

# 1) Generate stats with a quality and filter breakdown
vcf-stats \
  file.vcf.gz \
  -f FILTER,QUAL=10:200 \
  -p out/

# 2) Generate stats for a single sample
vcf-stats \
  file.vcf.gz \
  -f SAMPLE/NA00001/DP=1:200 \
  -p out/

# 3) Save a dump that can be replayed later
vcf-stats file.vcf.gz > perl.dump

Recommended Workflow

1. Start from a gzipped VCF and decide whether you want all samples or a subset with -s.
2. Specify one or more filter expressions with -f to control which summaries are produced.
3. Use -p to keep outputs grouped in a predictable directory or prefix.
4. Review the generated summaries before turning them into dashboards or QC gates.

Guardrails

• Input is expected to be a gzipped VCF.
• -f expressions are powerful but easy to misuse; double-check field paths like INFO/INDEL or SAMPLE/NAME/DP.
• Excluding irrelevant samples with -s can materially improve runtime on large cohorts.
• This tool does not provide a normal --version path; use -h for interface confirmation.