The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples.

• hap-ibd GitHub page

• Module Name: hap-ibd (see the modules page for more information)
• Unusual environment variables set
  • HAPIBD_BIN       executable directory
  • HAPIBD_DATA  sample data directory
  • JARPATH  path to the folder containing JAR file

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

[user@biowulf]$ sinteractive
[user@cn3335 ~]$ module load Hap-IBD
[+] Loading java 12.0.1  ...
[+] Loading Hap-IBD  20221201
[user@cn3335 ~]$ hap-ibd
hap-ibd.jar  [ version 1.0, 20May22.818 ]

Syntax: java -jar hap-ibd.jar [arguments in format: parameter=value]

Data Parameters:
  gt=<VCF file with GT field>                         (required)
  map=<PLINK map file with cM units>                  (required)
  out=<output file prefix>                            (required)
  excludesamples=<excluded samples file>              (optional)

Algorithm Parameters:
  min-seed=<min cM length of seed segment>            (default: 2.0)
  max-gap=<max base pairs in non-IBS gap>             (default: 1000)
  min-extend=<min cM length of extension segment>     (default: min(1.0, min-seed))
  min-output=<min cM length of output segment>        (default: 2.0)
  min-markers=<min markers in seed segment>           (default: 100)
  min-mac=<minimum minor allele count filter>         (default: 2)
  nthreads=<number of computational threads>          (default: all CPU cores)
[user@cn3335 ~]$ cp $HAPIBD_DATA/* .
[user@cn3335 ~]$ hap-ibd gt=target.truth.vcf.gz map=target.map out=hap-ibd.out
Copyright (C) 2019 Brian L. Browning
Enter "java -jar hap-ibd.jar" to print a list of command line arguments

Program            :  hap-ibd.jar  [ version 1.0, 20May22.818 ]
Start Time         :  11:21 AM EST on 31 Jan 2023
Max Memory         :  30688 MB

Parameters
  gt               :  target.truth.vcf.gz
  map              :  target.map
  out              :  hap-ibd.out
  min-seed         :  2.0
  max-gap          :  1000
  min-extend       :  1.0
  min-output       :  2.0
  min-markers      :  100
  min-mac          :  2
  nthreads         :  24

Statistics
  samples          :  300
  markers          :  24965
  IBD segments     :  181
  IBD segs/sample  :  0.6
  HBD segments     :  0
  HBD segs/sample  :  0.000

Wallclock Time:    :  2 seconds
End Time           :  11:21 AM EST on 31 Jan 2023