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.TH "ABBA-BABA" "1" "" "abba-baba (vcflib)" "abba-baba (VCF genotype)"
.hy
.SH NAME
.PP
\f[B]abba-baba\f[R]
.SH SYNOPSIS
.PP
\f[B]abba-baba\f[R] \[en]tree 0,1,2,3 \[en]file my.vcf \[en]type PL
.SH DESCRIPTION
.PP
\f[B]abba-baba\f[R] calculates the tree pattern for four indviduals.
This tool assumes reference is ancestral and ignores non
\f[B]abba-baba\f[R] 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.
.SH OPTIONS
.IP
.nf
\f[C]

     Example:
     D   C  B   A 
     \[rs] /  /    /  
      \[rs]  /    /   
       \[rs]    /    
        \[rs]  /     
         /        
        /         
 --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
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.