SNP tools for Microsoft Excel  (last updated in Oct. 18, 2012)

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SNP tools is a general add-in for Microsoft Excel to do data conversion and basic analysis for Single Nucleotide Polymorphism (SNP) data.

SNP tools enhances the ability of MS-Excel for genetic and epidemiological functions, such as the calculation of odds ratio (OR), confidence interval (CI), p-value, and power. SNP tools can convert your laboratorial data in Excel to the format of Haploview, Plink, Merlin, SNPHAP, Phase and PedPhase for the further analysis.

SNP tools for MS-Excel can be used for MS-Excel 2000-2011 in MS-Windows 2000, XP, Vista, and Windows 7. The Mac OS X version for MS-Excel 2011 is also available.


Install and uninstall SNP tools

Download: SNP tools (V1.80) for MS-Windows, SNP_tools_Mac (V1.70) for Mac OS X

Install SNP tools in MS-Windows 2000-XP and MS-Excel 2000-2003

Install SNP tools in MS-Windows Vista, Windows 7 and MS-Excel 2007 and 2010

Install SNP tools in MS-Excel for Mac 2011

Uninstall SNP tools

Important: You might need to adjust your security level to "Medium" in the table of "Security level" of "tools- Macro-Security" in Excel, if your system refuses to accept the Add-ins. In the new update version of SNP tools, a certificate was added by a digital signature, making installation friendlier. The medium security level arrows you to decide whether enable a "Enable" button in the window of "Security Warning".


In some systems it might require users to download and register Common dialogue runtime library and RefEdit by themselves (or see following install guide)

How to install Common dialogue runtime library

How to solve problem of missing RefEdit

How to let SNP tools automatically run Haploview, Phase and SNPHAP


Usage of SNP_tools

An Example file with input data and the usage of SNP built-in functions

How to convert your own SNP data into the formats of Haploview and Plink

How to convert Affymetrix chip data into the format of Haploview and Plink

Usage of some frequent used built-in functions:

ORMH =strata_OR(B4:E5) (MH = Mantel Haenszel strata calculation)
X2MH =strata_OR_x2(B4:E5)
PMH =strata_OR_P(B4:E3)

Downstream analysis software



We compiled the source code of SNPHAP for Linux in cygwin thus it can be run in DOS/MS-Windows. Here is the SNPHAP for DOS/MS-Windows and the cygwin dll.



How to download genotype file from HAPMAP and convert into Haploview formats.

How to download HapMap (HapMart 0.7) and convert into Haploview format by SNP tools 



Full Text download

Chen, B., et al., SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel. BMC Res Notes, 2009. 2(1): p. 214.


Release Notes


Questions and Help Requests

SNP tools was mainly developed in Windows XP (Windows 2000) + MS-Excel 2003. It works well in Windows 7 and MS-Excel 2007 now. If any problems running in special platform, please feel free to let us know: or