We downloaded the phased data from 
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/
working/20130723_phase3_wg/shapeit2/

We inferred short IBD segments using Beagle's Refined IBD 
(b4.r1230.jar) using the phased data.  For each pair of 
individuals, we filled short gaps between segments using 
an algorithm that will be described in detail elsewhere.  
CentiMorgan lengths were determined using the genetic maps 
produced by the HapMap consortium.  After filling short gaps
in IBD, the IBD was recorded on an individual level, rather
than a haplotype level.  Thus identical twins and parent-
offspring pairs would be expected to share around 3300 cM of 
IBD autosome-wide.  Full-sibs would be expected to share 
around 3300*0.75=2475 cM, while half-sibs and avuncular pairs 
would share around 3300*0.5=1650 cM. IBD segments of size 5 cM 
and longer were retained.

The autosomal_ibd_by_pair.txt file contains all pairs of 
individuals with at least one retained autosomal IBD segment.  
The first and third columns give the individuals' IDs.  The 
second and fourth columns give the individuals' populations.  
The fifth column gives the sum of the lengths of the retained 
autosomal IBD segments.  

The chrX_ibd_by_pair.txt file has the same format, but is for 
chromosome X IBD.

Sharon Browning and Brian Browning. August 27, 2014.