vcf-to-tab

name	vcf-to-tab
description	Use when converting VCF genotype data to simple tabular format for downstream analysis or reporting.
disable-model-invocation	true
user-invocable	true

vcf-to-tab

Quick Start

• Command: vcf-to-tab [OPTIONS] < in.vcf > out.tab
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-to-tab
• Full reference: See references/help.md

When To Use This Tool

• Convert a streamed VCF into a simple tabular representation quickly.
• Emit IUPAC-coded alleles if that specific output style is needed.
• Keep using it only in legacy vcftools-style stream pipelines; for new work, prefer bcftools query.

Common Patterns

# 1) Convert a plain VCF stream to tab
cat input.vcf | vcf-to-tab > out.tab

# 2) Use IUPAC ambiguity codes
cat input.vcf | vcf-to-tab -i > out.iupac.tab

Recommended Workflow

1. Stream a valid VCF into stdin.
2. Decide whether ambiguity codes are needed with -i.
3. Write the tabular output to a file and inspect a few lines for column expectations.
4. Move to bcftools query if the output specification starts to become more complex than this script can express.

Guardrails

• This is a deprecated vcftools utility; bcftools query is the preferred modern replacement.
• Input is stdin-driven and output is stdout-driven.
• --version is not supported in the usual way; use -h for interface help.
• Because the format is simple and opinionated, do not expect the field-level flexibility of bcftools query.