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An ultra-fast computational pipeline that searches for multiple single nucleotide variants (SNVs) that are scaffolded by the same reads. We refer to scaffolded SNVs as local haplotypes (LH). When an LH exhibits more than two genotypes, we call it a local haplotype variant (LHV). The presence of LHVs is considered evidence of somatic mosaicism because a genetically homogeneous cell population will not harbor LHVs.

Software type:
Command line interface
Restrictions to use:
Operating system:
Unix/Linux, Mac OS
Computer skills:
LocHap version 1.0
g++ compiler, GNU Make.
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  • Subhajit Sengupta <subhajit06 at gmail.com>


Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA; Center for Molecular Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Department of Health Studies, University of Chicago, Chicago, IL 60637, USA

  • (Sengupta et al., 2015) Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples. Nucleic acids research.
    PMID: 26420835
  • (Spencer et al., 2014) Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. The Journal of molecular diagnostics.
    PMID: 24211364
  • (Stead et al., 2013) Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. Human mutation.
    PMID: 23766071
  • (Roberts et al., 2013) A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics.
    PMID: 23842810
  • (Wang et al., 2013) Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome medicine.
    PMID: 24112718

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