---
name: "abba-baba"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/abba-baba"
---

# abba-baba(1)

## NAME

**abba-baba**

## SYNOPSIS

**abba-baba** –tree 0,1,2,3 –file my.vcf –type PL

## DESCRIPTION

**abba-baba** calculates the tree pattern for four indviduals. This tool assumes reference is ancestral and ignores non **abba-baba** sites. The output is a boolian value: 1 = true , 0 = false for abba and baba. the tree argument should be specified from the most basal taxa to the most derived.

## OPTIONS

-

  ```
       Example:
       D   C  B   A
       \ /  /    /
        \  /    /
         \    /
          \  /
           /
          /
   --tree A,B,C,D
  Output : 4 columns :
       1. seqid
       2. position
       3. abba
       4. baba
  required: t,tree       -- a zero based comma separated list of target individuals corrisponding to VCF columns
  required: f,file       -- a properly formatted VCF.
  required: y,type       -- genotype likelihood format ; genotypes: GP,GL or PL;
  type: genotype
  ```

## EXIT VALUES

- **0**

  Success

- **not 0**

  Failure

## SEE ALSO

[**vcflib**(1)](/vcflib/1.md)

## OTHER

## LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

## AUTHORS

Erik Garrison and vcflib contributors.