title: fcGENE: a versatile tool for processing and transforming SNP datasets.
abstract: BACKGROUND
  Modern analysis of high-dimensional SNP data requires a number of biometrical and statistical methods such as pre-processing, analysis of population structure, association analysis and genotype imputation. Software used for these purposes often rely on specific and incompatible input and output data formats. Therefore extensive data management including multiple format conversions is necessary during analyses.
  
  
  METHODS
  In order to support fast and efficient management and bio-statistical quality control of high-dimensional SNP data, we developed the publically available software fcGENE using C++ object-oriented programming language. This software simplifies and automates the use of different existing analysis packages, especially during the workflow of genotype imputations and corresponding analyses.
  
  
  RESULTS
  fcGENE transforms SNP data and imputation results into different formats required for a large variety of analysis packages such as PLINK, SNPTEST, HAPLOVIEW, EIGENSOFT, GenABEL and tools used for genotype imputation such as MaCH, IMPUTE, BEAGLE and others. Data Management tasks like merging, splitting, extracting SNP and pedigree information can be performed. fcGENE also supports a number of bio-statistical quality control processes and quality based filtering processes at SNP- and sample-wise level. The tool also generates templates of commands required to run specific software packages, especially those required for genotype imputation. We demonstrate the functionality of fcGENE by example workflows of SNP data analyses and provide a comprehensive manual of commands, options and applications.
  
  
  CONCLUSIONS
  We have developed a user-friendly open-source software fcGENE, which comprehensively supports SNP data management, quality control and analysis workflows. Download statistics and corresponding feedbacks indicate that software is highly recognised and extensively applied by the scientific community.
authors: Medical Department, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; Medical Department, LIFE Research Center (Leipzig Interdisciplinary Research Cluster of Genetic Factors, Phenotypes and Environment), University of Leipzig, Leipzig, Germany.
authors: Nab Raj
authors: NR
authors: Roshyara
authors: Medical Department, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; Medical Department, LIFE Research Center (Leipzig Interdisciplinary Research Cluster of Genetic Factors, Phenotypes and Environment), University of Leipzig, Leipzig, Germany.
authors: Markus
authors: M
authors: Scholz
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012984:Software