vcf-convert

name	vcf-convert
description	Use when converting VCF files between format versions (4.0, 4.1, 4.2) for compatibility with downstream bioinformatics tools.
disable-model-invocation	true
user-invocable	true

vcf-convert

Quick Start

• Command: vcf-convert -v <4.0|4.1|4.2> [options] < in.vcf > out.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert
• Fallback launcher in this workspace: /home/vimalinx/miniforge3/envs/bio/bin/perl /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert
• Full reference: See references/help.md

When To Use This Tool

• Convert a VCF stream between versions 4.0, 4.1, and 4.2 for downstream compatibility.
• Upgrade older VCFs before handing them to newer tooling.
• Normalize indel representation during version conversion when you can provide the reference FASTA.
• Keep using it only if you already depend on the vcftools Perl helpers; for fresh pipelines, prefer modern bcftools-based normalization when possible.

Common Patterns

# 1) Upgrade an older SNP-only VCF to 4.2
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \
  -v 4.2 \
  < input.vcf > output.vcf

# 2) Convert an indel-containing VCF with a faidx-indexed reference
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \
  -v 4.2 \
  -r ref.fa \
  < input.vcf > output.vcf

# 3) Downgrade cautiously for an older consumer
/home/vimalinx/miniforge3/envs/bio/bin/perl \
  /home/vimalinx/miniforge3/envs/bio/bin/vcf-convert \
  -v 4.1 \
  < input.vcf > output.vcf

Recommended Workflow

1. Confirm which VCF version the downstream tool actually requires before converting anything.
2. Treat the input as a stream: feed it on stdin and capture the converted VCF from stdout.
3. Provide -r ref.fa whenever non-SNP variants are present so indel REF / ALT rewriting is well-defined.
4. Validate the output with a downstream parser or vcf-validator before swapping it into a pipeline.

Guardrails

• In this shell, direct invocation may fail with Can't locate Vcf.pm; activate the bio environment first or call the script through /home/vimalinx/miniforge3/envs/bio/bin/perl.
• The -v/--version option sets the target VCF format version; it is not a program-version flag.
• Downgrading VCF versions is explicitly marked upstream as experimental.
• Indel conversion needs a samtools-faidx indexed reference FASTA via -r.
• This tool reads from stdin and writes to stdout; it does not edit files in place.