---
name: "fill-aa"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fill-aa"
---

# fill-aa(1)

fill in ancestral alleles

## NAME

fill-aa - fill in ancestral alleles

## SYNOPSIS

**fill-aa \[OPTIONS\]**

## DESCRIPTION

-

  zcat file.vcf.gz \| fill-aa -a ancestral-alleles.fa.gz \| bgzip -c \> out.vcf.gz

## OPTIONS

- **-a** \<file.gz\>

  file containing acestral alleles