Recent changes to QuickIBD

QuickIBD modified by Guobo Chen

Guobo Chen — Mon, 10 Mar 2014 10:23:36 -0000

--- v4
+++ v5
@@ -7,7 +7,12 @@
 quick-ibd

 Example
+
+~~~~
 gear --quick-ibd --bfile test --out test
+~~~~
+
+[Donwload example files](https://sourceforge.net/p/gbchen/wiki/HELink/attachment/ibdtest.zip)

 Two files will be generated.
 One is test.ibd.raw, which only gives the parent specific ibd for informative loci.

QuickIBD modified by Guobo Chen

Guobo Chen — Sat, 08 Mar 2014 09:35:35 -0000

--- v3
+++ v4
@@ -32,4 +32,4 @@
 Illustrated example
 The left panel is for paternal IBD for a pair of siblings over 200 markers. From top to bottom are IBD as from informative markers (from *.ibd.raw), inferred from flanking markers (from *.ibd), and real IBD.
 The right panel is for maternal IBD.
-![Illustration](https://sourceforge.net/p/gbchen/wiki/QuickIBD/attachment/IBD.bmp)
+![Illustration](https://sourceforge.net/p/gbchen/wiki/QuickIBD/attachment/Fig1_IBD.jpeg)

QuickIBD modified by Guobo Chen

Guobo Chen — Mon, 03 Feb 2014 14:01:48 -0000

--- v2
+++ v3
@@ -32,4 +32,4 @@
 Illustrated example
 The left panel is for paternal IBD for a pair of siblings over 200 markers. From top to bottom are IBD as from informative markers (from *.ibd.raw), inferred from flanking markers (from *.ibd), and real IBD.
 The right panel is for maternal IBD.
-![Illustration](https://sourceforge.net/p/gbchen/wiki/QuickIBD/attachment/IBD.jpeg)
+![Illustration](https://sourceforge.net/p/gbchen/wiki/QuickIBD/attachment/IBD.bmp)

QuickIBD modified by Guobo Chen

Guobo Chen — Fri, 24 Jan 2014 08:57:10 -0000

--- v1
+++ v2
@@ -28,3 +28,8 @@
 10000 10004 10000 10003 -1.0 -1.0 -1.0 -1.0 -1.0 -0.6666666666666667 -0.3333333333333333 0.0 0.3333333333333333 0.6666666666666667 1.0 0.0 -1.0 -0.5 0.0 0.5 1.0 -1.0 0.0 1.0 
 10000 10004 10000 10003 1.0 0.3333333333333333 -0.3333333333333333 -1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 0.3333333333333333 -0.3333333333333333 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 0.0 
 ~~~~~~~
+
+Illustrated example
+The left panel is for paternal IBD for a pair of siblings over 200 markers. From top to bottom are IBD as from informative markers (from *.ibd.raw), inferred from flanking markers (from *.ibd), and real IBD.
+The right panel is for maternal IBD.
+![Illustration](https://sourceforge.net/p/gbchen/wiki/QuickIBD/attachment/IBD.jpeg)

QuickIBD modified by Guobo Chen

Guobo Chen — Fri, 24 Jan 2014 08:49:17 -0000

Quick IBD algorithm/Parent of origin IBD for nuclear families

It is a method to calculate parent of origin IBD given high dense markers. As recombination events are rare along a chromosome, with few informative loci, whose IBD information is known, it is easy to infer the IBD for a region given the known IBD at the flanking regions.

Command
quick-ibd

Example
gear --quick-ibd --bfile test --out test

Two files will be generated.
One is test.ibd.raw, which only gives the parent specific ibd for informative loci.
The other is test.ibd, which gives the inferred ibd for all loci.

Format for test.ibd.raw
The first and the second fields are family id and individual id for sibling 1, and the third and the forth fields are family id and individual id for sibling 2. Since the fifth column on, each column represents the ibd for a locus. -1 means not ibd, 0 for unknown, and 1 for ibd. Each pair of full sibling will show in two rows, for which the first is for paternal ibd and the second for maternal ibd.

10000 10004 10000 10003 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 -1.0 0.0 0.0 0.0 1.0 -1.0 0.0 1.0
10000 10004 10000 10003 1.0 0.0 0.0 -1.0 0.0 1.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 -1.0 0.0 0.0 0.0 -1.0 0.0 0.0

Format for test.ibd
In this file, the first four columns are the same as the test.ibd.raw. However, in this file the loci whose IBD are unknown (with value 0 in ibd.raw) is inferred with flanking ibd known loci.

10000 10004 10000 10003 -1.0 -1.0 -1.0 -1.0 -1.0 -0.6666666666666667 -0.3333333333333333 0.0 0.3333333333333333 0.6666666666666667 1.0 0.0 -1.0 -0.5 0.0 0.5 1.0 -1.0 0.0 1.0 
10000 10004 10000 10003 1.0 0.3333333333333333 -0.3333333333333333 -1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0 0.3333333333333333 -0.3333333333333333 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 0.0