fill-an-ac

name	fill-an-ac
description	Use when you need to populate or update AC (allele count) fields in VCF files from the vcftools suite.
disable-model-invocation	true
user-invocable	true

fill-an-ac

Quick Start

• Command: fill-an-ac < in.vcf > out.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/fill-an-ac
• Full reference: See references/help.md for complete options

When To Use This Tool

• Recalculate AC and AN INFO fields from genotype columns.
• Normalize VCFs that are missing allele-count metadata after genotype edits or sample filtering.
• Add fresh allele-count annotations before downstream frequency-based filtering or QC.

Common Patterns

# 1) Recalculate AC and AN from a VCF stream
fill-an-ac < input.vcf > output.vcf

# 2) Use an explicit input filename and bgzip the result
fill-an-ac input.vcf | bgzip -c > output.vcf.gz

Recommended Workflow

1. Start from a genotype-containing VCF with valid sample columns.
2. Run fill-an-ac from stdin or by passing a single input filename.
3. Inspect the header to confirm both AC and AN INFO definitions were added.
4. Spot-check a few sites before using the recalculated counts downstream.

Guardrails

• The script accepts either stdin or one filename argument; it is not stdin-only.
• --help works, but --version is not implemented and errors as an unknown parameter.
• The recalculation is hard-coded as recalc_ac_an(2), so it assumes diploid genotype counting.
• Existing AC / AN content is recomputed from genotypes rather than preserved verbatim.