abba-baba

       Erik Garrison and vcflib contributors.

abba-baba (vcflib)                                                                                  ABBA-BABA(1)

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.

0      Success

       not0  Failure

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

abba-baba

                   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

vcflib(1)

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