Provided by: libvcflib-tools_1.0.9+dfsg1-3build1_amd64 bug

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)


OTHER
LICENSE
       Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.  MIT licensed.


AUTHORS
       Erik Garrison and vcflib contributors.