- The software compares test HLA genotypes against reference HLA genotypes
- hlaGenotypeEvaluator assigned a score for each allele tested
-
For Windows computers, we recommend installing the Git Bash terminal (https://git-scm.com/download/win). The Git Bash terminal allows HaplObserve to be run the same way as in Linux and Mac terminals
-
Download and Install Java SE Development Kit (JDK - 1.8 or newer)
-
Download jar file (https://github.com/kosoegawa/hlaGenotypeEvaluator/releases/download/v1.0.0/hlaGenotypeEvaluator-0.0.1-SNAPSHOT-jar-with-dependencies.jar)
-
alternatively, download can be made directly on a computer with this command:
- Input files can be Histoimmunogenetics Markup Language (HML: https://bioinformatics.bethematchclinical.org/hla-resources/hml/) or csv file format.
- The file extension of HML can be either ".xml" or ".hml".
- The HML report can be generated using commercially available NGS HLA genotyping software, such as MiaFora (Immucor), TypeStream Visual (One Lambda) or HLA Twin (Omixon)
- The reference HML contains "reference" report, and test HML includes test report
- The software takes <baseDirectory> as an argument. The <baseDirectory> name can be anything, such as validation, but do not use space in <baseDirectory> name.
- HML files must be stored in "ref" and "test" directories. The software requires the following directory and file structures:
- “<baseDirectory>/ref/XXX.xml”, “<baseDirectory>/ref/XXX.hml” or “<baseDirectory>/ref/XXX.csv”
- Input reference file (XXX) should be stored in “ref” directory, and "ref" directory name must be used.
- “<baseDirectory>/test/YYY.xml”, “<baseDirectory>/test/YYY.hml” or “<baseDirectory>/test/YYY.csv”
- Input test file (YYY) should be stored in “test” directory, and "test" directory name must be used.
- Only one HML file should be stored in each "ref" and "test" directories.
- The software can be executed as follows:
- java -jar hlaGenotypeEvaluator-0.0.1-SNAPSHOT-jar-with-dependencies.jar <baseDirectory>
- The output file is generated in “/TestResult_today.csv". The file name will have today's date.
- This software takes csv files as input files, and generates csv output file as follows:
- The first argument should be a file containing reference HLA genotypes (CSV file format)
- The second argument should be a file that contains test HLA genotypes to be evaluated (CSV file format)
- These files should be in the same format. The first column indicates "Sample ID", and the second column shows "GL String". These files should contain header in the first line
- The third argument should be provided to specify output file name. Date and ".csv" extension is added by the software
- The software can be executed as follows:
- java -jar hlaGenotypeEvaluator-0.0.1-SNAPSHOT-jar-with-dependencies.jar reference.csv test.csv testResult
- the software generates a result csv file
- Results consisted of a column for each allele and locus with 3 rows per sample.
- The first row represents the "Reference" HLA genotypes.
- The second row shows "Test" HLA genotypes.
- The third row contains "Score" for the comparison between the reference genotypes and the test genotypes for each locus
- The "Score" includes the following wording
- Identical: HLA genotypes are exactly identical
- Concordance: Both Test and Ref are concordant at least by two field assessment
- AmbResultConcordant: Ambiguity reported in the Test but not in the Reference
- AmbRefConcordant: Ambiguity reported in the Reference
- AmbRefAmbResultConcordant: Ambiguity reported in the Reference and Test
- UnresolvedNullAmbResultConcordant: Concordant, but Null allele was found in the Test ambiguity string
- Discordant: Indicates both alleles do not match at all
Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop [https://www.ncbi.nlm.nih.gov/pubmed/30738112]