VDJML: A file format with tools for capturing the results of inferring immune receptor rearrangements

Inimary T. Toby, Mikhail K. Levin, Edward A. Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. ScheuermannNancy Monson, Steven H. Kleinstein, Lindsay G. Cowell

Research output: Contribution to journalArticlepeer-review


Background: The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results: To help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions: The VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/. We welcome participation from the community in developing the file format standard, as well as code contributions.

Original languageEnglish
Pages (from-to)333-343
JournalBMC Bioinformatics
StatePublished - 6 Oct 2016
Externally publishedYes

Bibliographical note

Funding Information:
Development of VDJML was supported by a Burroughs Welcome Fund Career Award and an NIAID-funded R01 (AI097403) to LGC. Florian Rubelt and Sanchita Bhattacharya were supported, in part, by the Bioinformatics Support Contract (BISC) HHSN272201200028C and the National Institute of Allergy and Infectious Diseases grant U19 AI090019. SHK was supported, in part, by National Institute of Allergy and Infectious Diseases grant R01 AI104739. NTG was supported, in part, by a PhRMA foundation pre-doctoral informatics fellowship. JAVH received research support from the National Library of Medicine of the National Institutes of Health (T15 LM07056). Publication charges for this article were paid from AI097403 to LGC.

Publisher Copyright:
© 2016 The Author(s).


  • Antigen receptor repertoire
  • C++
  • Data sharing
  • Data standards
  • Immune repertoire
  • Python
  • Repertoire profiling
  • XML

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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