ABBA-BABA(1) abba-baba (VCF genotype) ABBA-BABA(1)

abba-baba

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

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.

     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

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vcflib(1)

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

Erik Garrison and vcflib contributors.

abba-baba (vcflib)