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LocHap: Local-Haplotype Variant Calling Software

Subhajit Sengupta, Kamalakar Gulutoka, Yitan Zhu, Yuan Ji*


Introduction:

We introduce local haplotype variants (LHVs) and a computational pipeline, LocHap, for calling LHVs. An LHV refers to a haplotype that manifests more than two alleles in a single human sample and consists of multiple proximal single nucleotide variants (SNVs). Since humans are diploid, having more than two alleles implies somatic mosaicism. i.e., cells are genetically heterogeneous in the sample due to somatic mutations. Using deep DNA-Seq data, we demonstrate by direct observations and rigorous statistical inference the existence of wide spread LHVs in human normal tissues and tumors, with higher frequencies of LHVs observed in tumor samples compared to normal, and older healthy individuals compared to younger healthy individuals. LocHap is ultrafast, open-source, and freely available to download. Recognition of the existence of LHVs in normal and disease samples could fundamentally change our practice in disease diagnosis, association, and prognosis.

LocHap is currently licensed under the GPL version 3, LocHap may be distributed under GPL version 3.

Citation:

      Sengupta, Subhajit, et al. "Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples."¬†Nucleic acids research¬†(2015): gkv953.

Here is the pre-print of our Local Haplotype paper.

Contact:

      Subhajit Sengupta: subhajit06@gmail.com ;  Yuan Ji: koaeraser@gmail.com

Software:

  • Version 2.0 release - 02/11/2016
  • In this version of LocHap we have
    • fixed dynamic memory allocation issues
    • fixed a bug related to final LH segment that appeared at the end of the VCF file
    Also in this version we provide few plugin scripts
    • to convert a HCF format file to a BED format file
    • to add homozygous SNVs in between and outside(distance specified by users) the existing heterozygous SNVs for each LH segment
    • to generate a script automatically to run LocHap for all the samples in the VCF file
    • [ Download Software ]    MD5 Checksum : 4268cc59cb94da8233751668de754e8b

  • Version 1.0 release update - 09/08/2014
    • This update contains a local cmake installer. Users who do not have cmake previously installed on their computer are recommended to use this version.
  • Version 1.0 release - 08/14/2014
    • LocHap is programmed using C++. Installation of LocHap requires g++ compiler and GNU Make (ftp://ftp.gnu.org/gnu/). For mac OSX, installing Xcode (IDE for Apple's OSX and iOS) would automatically install those tools.
    • We have tested LocHap on mac OSX 10.8.4 and 10.9, CentOs 6.5, and Ubuntu 12.04.4 LTS. Presently we have not tested our software on any Windows operating system.
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