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.\" Automatically generated by Pandoc 2.19.2
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.\" Define V font for inline verbatim, using C font in formats
.\" that render this, and otherwise B font.
.ie "\f[CB]x\f[]"x" \{\
. ftr V B
. ftr VI BI
. ftr VB B
. ftr VBI BI
.\}
.el \{\
. ftr V CR
. ftr VI CI
. ftr VB CB
. ftr VBI CBI
.\}
.TH "ABBA-BABA" "1" "" "abba-baba (vcflib)" "abba-baba (VCF genotype)"
.hy
.SH NAME
.PP
\f[B]abba-baba\f[R]
.SH SYNOPSIS
.PP
\f[B]abba-baba\f[R] \[en]tree 0,1,2,3 \[en]file my.vcf \[en]type PL
.SH DESCRIPTION
.PP
\f[B]abba-baba\f[R] calculates the tree pattern for four indviduals.
This tool assumes reference is ancestral and ignores non
\f[B]abba-baba\f[R] 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.
.SH OPTIONS
.IP
.nf
\f[C]
Example:
D C B A
\[rs] / / /
\[rs] / /
\[rs] /
\[rs] /
/
/
--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
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.
MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
.SH AUTHORS
Erik Garrison and vcflib contributors.
|
