OptiType pipeline

OptiType specifications

Information


Unique identifier OMICS_05461
Name OptiType
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline András Szolek <>

Publication for OptiType

OptiType IN pipelines

 (2)
2018
PMCID: 5834292
PMID: 29541393
DOI: 10.18632/oncotarget.24232

[…] variant depth of ≥4, (iv) variant frequency in tumor of ≥10%, (v) variant frequency in normal of <2%, and (vi) fisher p value of <0.05. hla class i genotypes of the tumor were determined by optitype algorithm using whole-exome sequence data of normal dnas [45]. potential neoantigens were predicted for each non-synonymous mutation by testing all 8- to 11-mer peptides harboring the amino […]

2018
PMCID: 5922371
PMID: 29721177
DOI: 10.18632/oncotarget.24867

[…] ≥10%, (v) variant frequency in normal of <2%, and (vi) fisher p value of <0.05., using whole-exome sequence data of the germline dnas, hla class i genotypes of each patient were determined by optitype algorithm [23]. subsequently, neoantigens for each hla allele were predicted from non-synonymous mutations identified through the whole exome sequence data of 14 tumor samples. all 8- […]

OptiType institution(s)
Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, and CeGaT GmbH, Tübingen, Germany

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