Usage

Ant and log4j are required for installation here. Download log4j from here. After installing ant, extract the archive using tar xvzf hla_ibd.tar.gz from the command line. Enter the extracted directory and build the jar using ant jar. This creates the hlaibd.jar file. This file and the downloaded log4j jar file should be included in the classpath for running the application.
Invocation

Use the command java -cp iplab.hla.HLAIBDMain for invocation

The following inputs should be passed

* GERMLINE matches file
* HLA types file. File containing the HLA type information. Sample file here

* Chromosome span start
* Chromosome span end
* This region will be used for determining the IBD matches which will be part of the graph. Testing was done using the chromosomal region spanning 100kb upstream to 100kb downstream of the HLA gene being analyzed. Output file name

Output

Sample output
INDIVIDUAL RESOLVED-STATUS TYPES
884M02 1 101 301
884F02 2 201 101 301 1501
884C04M 3 2501

The resolved status is defined as follows

1. Individual assigned both the HLA types
2. Ambiguous resolution: First type in the list is assigned as one of the HLA types. The second HLA type is predicted to be any one of the listed files.
3. Individual could be homozygous in the listed type.