vcf-consensus

name	vcf-consensus
description	Use when applying VCF variants to a reference FASTA to generate a consensus sequence.
disable-model-invocation	true
user-invocable	true

vcf-consensus

Quick Start

• Command: cat ref.fa | vcf-consensus [OPTIONS] in.vcf.gz > out.fa
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-consensus
• Full reference: See references/help.md

When To Use This Tool

• Apply variants from a VCF onto a reference FASTA to create a consensus sequence.
• Produce sample-specific consensus from a multi-sample VCF.
• Emit haplotype-specific consensus or IUPAC-coded ambiguity consensus.
• Use it for targeted region reconstruction after extracting the exact reference segment you want.

Common Patterns

# 1) Apply all variants to a reference segment
samtools faidx ref.fa chr1:1000-2000 \
  | vcf-consensus calls.vcf.gz \
  > consensus.fa

# 2) Make sample-specific consensus
samtools faidx ref.fa chr1:1000-2000 \
  | vcf-consensus -s SAMPLE1 calls.vcf.gz \
  > sample1.consensus.fa

# 3) Emit haplotype 1 or IUPAC consensus
samtools faidx ref.fa chr1:1000-2000 \
  | vcf-consensus -H 1 calls.vcf.gz \
  > hap1.fa

Recommended Workflow

1. Decide which reference interval or contig you actually want to reconstruct.
2. Stream the matching FASTA sequence into stdin, ideally using samtools faidx.
3. Apply variants from the compressed VCF with optional sample or haplotype selection.
4. Inspect the resulting FASTA header and sequence length before treating it as final biological truth.

Guardrails

• Reference FASTA comes from stdin; the tool does not read the FASTA by filename.
• The usual usage expects a compressed .vcf.gz.
• For targeted consensus, the FASTA header is expected in >chr:from-to style when using region slices.
• If the VCF has multiple samples, omitting -s applies all variants together, which is often not what you want.