vimalinx 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
- Ensure your VCF file is valid and contains SNP variants
- Pipe the VCF to the tool:
cat file.vcf | vcf-tstv - Review the reported Ts/Tv ratio
- 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
-hfor 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