vcf-query

name	vcf-query
description	Use when extracting and formatting specific fields from compressed VCF files, querying variants by region, or generating custom tabular output with genotype and INFO data.
disable-model-invocation	true
user-invocable	true

vcf-query

Quick Start

• Command: vcf-query [OPTIONS] file.vcf.gz
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-query
• Full reference: See references/help.md

When To Use This Tool

• Extract selected VCF fields into a custom tabular report.
• Loop over per-sample genotype fields with bracket expressions.
• Run quick region-restricted queries on an indexed .vcf.gz.
• Keep using it only if you already depend on the vcftools Perl utility; for new workflows, prefer bcftools query.

Common Patterns

# 1) Extract core variant fields plus depth
vcf-query \
  file.vcf.gz \
  -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/DP\n'

# 2) Emit per-sample genotype information
vcf-query \
  file.vcf.gz \
  -f '%CHROM:%POS[\t%SAMPLE=%GT]\n'

# 3) Restrict output to a region
vcf-query \
  file.vcf.gz \
  -r 1:1000-2000 \
  -f '%CHROM\t%POS\t%FILTER\n'

Recommended Workflow

1. Start by listing available columns with -l if the file provenance is unclear.
2. Build the output format string deliberately with %INFO/TAG, %GT, %SAMPLE, and bracket loops when sample iteration is needed.
3. Restrict to a genomic interval with -r only when the file is properly indexed.
4. Redirect output to a file or pipe it into downstream table-processing tools.

Guardrails

• Input files are expected to be compressed VCFs, and region queries require tabix indexing.
• This script is explicitly marked upstream as not being supported in the future; prefer bcftools query for durable pipelines.
• The default format string already loops over samples, so be explicit with -f if you want predictable output.
• -c/--columns can take either a comma-separated list or a file of one column name per line.