ABBA-BABA

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.