1% ABBA-BABA(1) abba-baba (vcflib) | abba-baba (VCF genotype)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**abba-baba**
7
8# SYNOPSIS
9
10**abba-baba** --tree 0,1,2,3 --file my.vcf --type PL
11
12# DESCRIPTION
13
14**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.
15
16
17
18# OPTIONS
19
20```
21
22
23     Example:
24     D   C  B   A
25     \ /  /    /
26      \  /    /
27       \    /
28        \  /
29         /
30        /
31 --tree A,B,C,D
32
33Output : 4 columns :
34     1. seqid
35     2. position
36     3. abba
37     4. baba
38required: t,tree       -- a zero based comma separated list of target individuals corrisponding to VCF columns
39required: f,file       -- a properly formatted VCF.
40required: y,type       -- genotype likelihood format ; genotypes: GP,GL or PL;
41
42
43type: genotype
44
45```
46
47
48
49
50
51# EXIT VALUES
52
53**0**
54: Success
55
56**not 0**
57: Failure
58
59# SEE ALSO
60
61
62
63[vcflib](./vcflib.md)(1)
64
65
66
67# OTHER
68
69## Source code
70
71[abba-baba.cpp](https://github.com/vcflib/vcflib/blob/master/src/abba-baba.cpp)
72
73# LICENSE
74
75Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
76
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