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 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS

Erik Garrison and vcflib contributors.