vcf-contrast

name	vcf-contrast
description	Use when comparing variant samples against background samples to identify unique genotypes and novel variants in VCF files.
disable-model-invocation	true
user-invocable	true

vcf-contrast

Quick Start

• Command: vcf-contrast +<variant_samples> -<background_samples> [OPTIONS] file.vcf.gz
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-contrast
• Full reference: See references/help.md

When To Use This Tool

• Contrast one sample group against another within a multi-sample VCF.
• Identify sites where case or focal samples carry genotypes or alleles absent from background samples.
• Add NOVELGT, NOVELAL, and NOVELTY INFO annotations for downstream filtering or reporting.
• Perform quick cohort-difference scans without writing a custom comparison script.

Common Patterns

# 1) Find variants present in A,B but absent from C,D,E
vcf-contrast \
  +A,B \
  -C,D,E \
  cohort.vcf.gz

# 2) Report only sites with novel genotypes
vcf-contrast \
  -n \
  +cases1,cases2 \
  -controls1,controls2,controls3 \
  cohort.vcf.gz

# 3) Require minimum depth and respect FILTER status
vcf-contrast \
  +tumor \
  -normal \
  -d 10 \
  -f \
  cohort.vcf.gz

Recommended Workflow

1. Prepare a bgzip-compressed VCF file containing all samples to be compared
2. Identify the samples expected to have unique variants (+) and the background control samples (-)
3. Run vcf-contrast +A,B -C,D,E [OPTIONS] file.vcf.gz with flags such as -n to output only novel sites or -f to apply filters
4. Pipe output to vcf-query or other tools to extract and format the annotated fields of interest

Guardrails

• Both variant sample list (+) and background sample list (-) are required arguments
• Input VCF must be bgzip-compressed with .vcf.gz extension
• Haploid genotypes are internally treated as homozygous diploid; "0/1" and "1" are considered different genotypes
• -n limits output to novel sites only; without it, the tool still emits all records, just with additional INFO annotations
• -f discards rows whose FILTER is neither PASS nor ., which changes the comparison universe before novelty is computed