%0 Journal Article
%T SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel
%A Bowang Chen
%A Stefan Wilkening
%A Marion Drechsel
%A Kari Hemminki
%J BMC Research Notes
%D 2009
%I BioMed Central
%R 10.1186/1756-0500-2-214
%X The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis).Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software.The completion of the human genome sequence and the ensued HapMap project has brought a wealth of data on genetic variation in the form of single nucleotide polymorphisms (SNPs) and more recently of copy number variants. These data are accessible through public data bases, such as HapMap [1] or the Cancer Genetic Markers of Susceptibility [2]. As a consequence, SNP genotyping has become a major activity for studies of disease susceptibility and pharmacogenetics. To analyze the data obtained from databases or from own studies, a large number of programs are used, but the first hand SNP data is often entered in or saved in the MS-Excel format. MS-Excel is a good general platform to edit limited amount of data (255 columns and 65,536 rows in MS-Excel 2003) and to do some basic statistical analysis, but it lacks genetic and epidemiological related functions. We developed an MS-Excel add-in, called SNP_tools, to facilitate basic genetic and epidemiological analysis, such as the calculation of odds ratio (OR), confidence interval (CI) p-value, and power.To further analyze the genotyping data, different programs might be used, for example: Haploview [3], Phase [4], SNPHAP [5], fastPHASE [6], Merlin [7], Plink [8], LdCompare [9] SNPassoc [10], and SPSS (SPSS Inc. Chicago, IL). Since each program has its own requirements for input files there is a need to convert data from one format to another.SNP_tools is implemented in Visual Basic for Application (VBA) in MS-Excel. It can run on MS-Excel 2000-200
%U http://www.biomedcentral.com/1756-0500/2/214