ABBA-BABA(1)

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.