Name: ImmunogeneticDataTools
Owner: NMDP/Be The Match Bioinformatics Research
Description: Immunogenetic Data Tools related to HLA, GLStrings, Linkage Disequilibrium
Created: 2014-11-27 03:58:23.0
Updated: 2017-03-28 22:22:02.0
Pushed: 2017-04-08 03:20:54.0
Homepage: null
Size: 13912
Language: Java
GitHub Committers
User | Most Recent Commit | # Commits |
---|
Other Committers
User | Most Recent Commit | # Commits |
---|
Linkage disequilibrium is the non-random association of alleles at two or more loci, that descend from a single ancestral chromosome. The particular linkages referenced here are relevant in the context of HLA and immunogenetics.
HLA typing using Next Generation Sequencing (NGS) is becoming common practice in research and clinical lab settings. HLA typing miss-call occurs when DNA sequences from one of the alleles drop out.
HLA Linkage Disequilibrium Validation software was developed to identify common linkages between HLA-B and HLA-C, and HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1 and HLA-DQB1. This information is useful when HLA typing from NGS is reviewed. The software not only validates known linkages, but also sends warning messages when unusual linkage was found.
The software user can find stronger evidences of the accuracy of his/her HLA typing results when common linkages are found. Also the user can focus on reviewing the unusual HLA linkages whether these are true or likely generated from DNA sequencing drop-outs.
The results of the software should be used for supporting the evidence, but not used to correct any HLA typing without confirmatory experiments.
Input: Genotype(s) - expressed as GL String
Output: Linked alleles by locus, a frequency and any additional notes, accompanied by GL String and Id (either assigned or generated)
Future Goals:
Using the software:
As of release .7, the ability to download the software package and make use of command line tools is available.
From the Releases section of GitHub you may grab the snapshot of the latest release. E.g: ld-tools-0.0.1-SNAPSHOT-bin.zip from release .7 at Releases
After un-zipping the software, you may run ./ld-tools-0.0.1-SNAPSHOT/bin/analyze-gl-strings -h for instructions on how to run the software.
Basic Installation Process from source code:
If you prefer to compile / package the software from source, follow these instructions…
Running a Test Data Set:
Properties:
Name: org.dash.frequencies
Value(s): wiki, nmdp-2007 (nmdp-2007-std), nmdp (nmdp-std)
Description: Specifies the desired frequency set
Note: The 2011 NMDP Frequencies (if specifying 'nmdp') are associated with a license agreement, specifying the allowance of use for research, but disallowing re-distribution. If you wish to use the 2011 NMDP Frequencies, you'll need to install them in your local repository by following the frequency install instructions at the bottom of this file.
Name: org.dash.hladb
Value(s): 3.25.0, 3.24.0, 3.23.0, 3.22.0, 3.21.0, 3.20.0, 3.19.0, 3.18.0, 3.15.0, 3.12.0, 3.11.0, 3.10.0, 3.9.0, 3.8.0, 3.7.0, 3.6.0, 3.5.0, 3.4.0, 3.3.0, 3.2.0, 3.1.0, 3.0.0
Description: Specifies the HLA DB version against which to validate common well documented alleles
Name: org.dash.ars
Value(s): hladb
Description: If specified, applies the antigen recognition site mappings from the HLA DB property specified. Otherwise, uses the antigen recognition site mappings associated with the NMDP 2011 frequencies
Name: org.dash.linkages
Value(s): acb, cb, drb_dq, drb_dqb, drb1_dqb1, fiv_loc, six_loc
Description: Specifies the loci across which to detect linkages using provided frequencies
Name: java.util.logging.config.file
Value(s): logging.properties
Logs:
2011 NMDP Frequency Install Instructions:
2011 NMDP Frequency Re-Formatting Instructions: