About SEQLinkage

SEQLinkage implements a collapsed haplotype pattern (CHP) method to generate markers from sequence data for linkage analysis. The core concept is that instead of treating each variant a separate marker, we create regional markers for variants in specified genetic regions (e.g. genes) based on haplotype patterns within families, and perform linkage analysis on markers thus generated. SEQLinkage takes sequence data in VCF format and perform two-point linkage analysis. It reports both LOD and HLOD scores for linkage analysis of multiple families. For more information please read the SEQLinkage manuscript and documentation.


The method and software was developed by Gao T. Wang, Di Zhang and Suzanne M. Leal at Baylor College of Medicine.

Why SEQLinkage

  • SEQLinkage implements a novel approach (the CHP method) to use sequence data for linkage analysis. Compare with applying traditional linkage methods directly to sequence data, our approach has a substantial gain in statistical power in the presence of intra- and inter-family allelic heterogeneity.
  • SEQLinkage supports output of CHP coded regional marker data to formats compatible with other linkage programs, reviving them for use in the next-generation sequencing era.
  • SEQLinkage can perform two-point linkage analysis using the CHP method, generating user-friendly output summary of analysis results in HTML format with tables and graphs.
  • SEQLinkage calculates HLOD scores for linkage analysis involving multiple families, thus automatically maximizing the linkage signal across families to allow for the presence of locus heterogeneity.
  • We recommend the use of SEQLinkage in conjunction with filtering based variant prioritization method in the analyses of sequence data of human pedigrees.

Ready to explore? Please take a look at Chapter 1 of SEQLinkage documentation to get familiar with the software interface, and work through Chapter 2 for a simple example data analysis using the software.


  • 2016.04.08 Version 1.0.0, various bug fixes and move source code to github
  • 2014.04.28 Version 1.0 alpha, first public release of SEQLinkage
  • 2014.04.02 Version 0.0.4, integrated linkage analysis pipeline
    • graphic summary and table output for linkage analysis results in HTML format
    • numerous bug fixes and optimizations
  • 2014.01.28 Version 0.0.3, move implementation of core algorithms from Python to C++
    • algorithms including Mendelian error check, genetic haplotyping, LD blocks computation and combined haplotype pattern coding method
  • 2013.12.19 Version 0.0.2, replace variant tools backbone with tabix library
  • 2013.11.25 Version 0.0.1, first release on institutional internal website
  • 2013.10.17 Draft version, completed for in-house data analyses

How to Cite SEQLinkage

Gao T. Wang, Di Zhang, Biao Li, Hang Dai and Suzanne M. Leal, Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data. European Journal of Human Genetics. In Press (2015)

Special Acknowledgment

Development of SEQLinkage was supported by the Centers for Mendelian Genomics. We thank Dr. Daniel Weeks, Dr. Jeff O'Connell (pedcheck program) and Dr. Alejandro Schaffer (FASTLINK package) for the permission to recompile the source code of their programs and to publish the binaries on this website.

SEQLinkage Forum

We welcome user input to the software and exchange of experiences on linkage analysis using sequence data. We encourage you to join the SEQLinkage users community by interacting with the developers and users on github.