title: SNP calling using genotype model selection on high-throughput sequencing data.
abstract: BACKGROUND
  A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.
  
  
  RESULTS
  A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers.
  
  
  BACKGROUND
  The GeMS package can be downloaded from https://sites.google.com/a/bioinformatics.ucr.edu/xinping-cui/home/software or http://computationalbioenergy.org/software.html.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China.
authors.forename: Na
authors.initials: N
authors.lastname: You
authors.forename: Gabriel
authors.initials: G
authors.lastname: Murillo
authors.forename: Xiaoquan
authors.initials: X
authors.lastname: Su
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zeng
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.forename: Kang
authors.initials: K
authors.lastname: Ning
authors.forename: Shoudong
authors.initials: S
authors.lastname: Zhang
authors.forename: Jiankang
authors.initials: J
authors.lastname: Zhu
authors.forename: Xinping
authors.initials: X
authors.lastname: Cui
mesh_terms: D000465:Algorithms; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D012984:Software; D046968:Thermoanaerobacter / Q000235:genetics