Vcf Query

# 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.