Biowulf High Performance Computing at the NIH
RefinedIBD: accurate and efficient identity-by-descent detection in population data

Refined IBD is a software package that detects identity-by-descent segments in phased genotype data. It achieves both computational efficiency and highly accurate IBD segment reporting by searching for IBD in two steps. The first step (identification) uses the GERMLINE algorithm to find shared haplotypes exceeding a length threshold. The second step (refinement) evaluates candidate segments with a probabilistic approach to assess the evidence for IBD.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn3200 ~]$module load RefinedIBD 
[+] Loading RefinedIBD / 12Jul18  ...
[user@cn3200 ~]$ refibd
...
Copyright (C) 2014-2017 Brian L. Browning
Usage: java -jar refined-ibd.12Jul18.a0b.jar [arguments]

data input/output parameters ...
  gt=                       (required)
  out=                           (required)
  map=                 (optional)
  chrom=<[chrom] or [chrom]:[start]-[end]>           (optional)

  excludesamples=    (optional)
  excludemarkers=    (optional)

analysis parameters ...
  nthreads=                       (default: machine-dependent)
  window=                          (default=40.0)
  lod=       (default=3.0)
  length=    (default=1.5)
  trim=      (default=0.15)
  scale=                         (default: data-dependent)
Download test data:
[user@cn3200 ~]$ wget http://faculty.washington.edu/browning/refined-ibd/test.refined-ibd.12Jul18.a0b.vcf.gz
--2019-01-14 10:02:27--  http://faculty.washington.edu/browning/refined-ibd/test.refined-ibd.12Jul18.a0b.vcf.gz
Resolving dtn05-e0 (dtn05-e0)... 10.1.200.241
Connecting to dtn05-e0 (dtn05-e0)|10.1.200.241|:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 190180 (186K) [application/x-gzip]
Saving to: ‘test.refined-ibd.12Jul18.a0b.vcf.gz’
Download genetic map:
[user@cn3200 ~]$ wget http://faculty.washington.edu/browning/refined-ibd/test.refined-ibd.12Jul18.a0b.genmap
--2019-01-14 10:05:48--  http://faculty.washington.edu/browning/refined-ibd/test.refined-ibd.12Jul18.a0b.genmap
Resolving dtn05-e0 (dtn05-e0)... 10.1.200.241
Connecting to dtn05-e0 (dtn05-e0)|10.1.200.241|:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 31056 (30K) [text/plain]
Saving to: ‘test.refined-ibd.12Jul18.a0b.genmap’
Run RefinedIBD analysis of the test data:
[user@cn3200 ~]$ refibd gt=test.refined-ibd.12Jul18.a0b.vcf.gz map=test.refined-ibd.12Jul18.a0b.genmap  out=out
refined-ibd.12Jul18.a0b.jar
Copyright (C) 2014-2017 Brian L. Browning
Enter java -jar refined-ibd.12Jul18.a0b.jar to list command line argument
Start time: 10:08 AM EST on 14 Jan 2019

Command line: java -Xmx27305m -jar refined-ibd.12Jul18.a0b.jar
  gt=test.refined-ibd.12Jul18.a0b.vcf.gz
  map=test.refined-ibd.12Jul18.a0b.genmap
  out=out

Samples:                 991        
Model scale:             3.15       

Window 1 (22:20002231-21998721)
Markers:                 675        
Model construction:      1 second
IBD detection:           2 seconds
Total time:              3 seconds

mean edges/level: 10     max edges/level: 22
mean edges/node:  1.424  mean count/edge: 198

Cumulative Statistics:

Markers:                 675        
Model construction:      1 second
IBD detection:           2 seconds
Total time:              4 seconds

End time: 10:08 AM EST on 14 Jan 2019
refined-ibd.12Jul18.a0b.jar finished
End the interactive session:
[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$