vcf-tstv

name	vcf-tstv
description	Use when you need to calculate the transition/transversion (Ts/Tv) ratio from VCF files for variant call quality assessment.
disable-model-invocation	true
user-invocable	true

vcf-tstv

Quick Start

• Command: cat file.vcf | vcf-tstv
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-tstv
• Reference: See references/help.md for full options

When To Use This Tool

• Compute a quick transition/transversion ratio from a VCF stream.
• Perform a lightweight QC sanity check on SNP callsets.
• Compare Ts/Tv behavior between filtered and unfiltered VCFs in a shell pipeline.
• Use a legacy vcftools helper when a simple one-number summary is enough.

Common Patterns

# 1) Calculate Ts/Tv from a plain VCF
cat file.vcf | vcf-tstv

# 2) Calculate Ts/Tv from a compressed VCF stream
gunzip -c file.vcf.gz | vcf-tstv

# 3) Evaluate Ts/Tv after an upstream SNP-only filter
bcftools view -v snps filtered.vcf.gz | vcf-tstv

Recommended Workflow

1. Ensure your VCF file is valid and contains SNP variants
2. Pipe the VCF to the tool: cat file.vcf | vcf-tstv
3. Review the reported Ts/Tv ratio
4. Compare against expected values for your sample type (e.g., ~2.0–2.1 for human whole-genome data)

Guardrails

• Accepts VCF input via stdin only; no file path arguments supported
• Only supports -h for help; no filtering or output formatting options
• Does not support --version; verify via bioconda/vcftools package info
• Treat the result as a rough QC metric; the expected Ts/Tv depends strongly on organism, assay, region selection, and filtering state
• For meaningful comparison, make sure upstream filtering and SNP selection are consistent across the callsets you compare