title: HomSI: a homozygous stretch identifier from next-generation sequencing data.
abstract: In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation, and in consanguineous families, several recessive disease genes have been discovered with the help of this technique. The researchers typically use single nucleotide polymorphism arrays to determine the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. Recently, the advent of next-generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf (variant call format) files as an input file, our program identifies the majority of homozygous regions found by microarray single nucleotide polymorphism genotype data.
  
  
  METHODS
  HomSI software is freely available at www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI, with an online manual.
authors.affiliation: Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK-BILGEM), 41470 Gebze, Kocaeli, Turkey and Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, 38039 Kayseri, Turkey.
authors.forename: Zeliha
authors.initials: Z
authors.lastname: Görmez
authors.forename: Burcu
authors.initials: B
authors.lastname: Bakir-Gungor
authors.forename: Mahmut Samil
authors.initials: MS
authors.lastname: Sagiroglu
mesh_terms: D003241:Consanguinity; D005808:Genes, Recessive; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006720:Homozygote; D006801:Humans; D020407:Internet; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D012984:Software