Man page - abba-baba(1)

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Package: libvcflib-tools
apt-get install libvcflib-tools

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libvcflib-tools

Manual

ABBA-BABA

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

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

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.