GMFilter is a Windows program for improving GeneMapper® analysis of 384 well SNPlex™ plates by removing bad wells, i.e. wells having a low signal intensity across all assays. This is done by creating a normal MS-DOS batch file, which deletes .fsa files of wells having a median signal intensity below a specified quality threshold. Afterwards the GeneMapper® analysis can be repeated with a standard analysis method (we recommend "RelaxedRules", see below).

GMFilter is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. GMFilter is not for commercial use.

When using please cite the following publication:
Teuber M, Wenz MH, Schreiber S, Franke A (2009).
GMFilter and SXTestPlate: software tools for improving the SNPlex(TM) genotyping system.
BMC Bioinformatics 10(1):81
PubMed (PMID:19267942)



GMFilter runs on all Windows platforms. It has not been tested under Windows Vista.

Important notes:

  • sample files in the Data Collection Software must have the following name format: PlateID_WellPosition (e.g. XR01-0001-4_A12.fsa)
  • run folders in the Data Collection Software must have the following name format: PlateID_PlateQuadrant_DateOfRun (e.g. XR01-0001-4_Q2_2007-01-01)
  • samples plot tables in GeneMapper® must have the following name format: PlateID_DateOfRun (e.g. XR01-0001-4_2007-01-01.txt)
  • plate barcode and run date in the samples plot file name must match names of run folders and .fsa files
  • save only exported samples plot tables (.txt) in the specified export folder



GMFilter installer (includes the application, online help and source code):
GMFilter_1_0_0_setup.exe (1,7 MB)

analysis methods for GeneMapper®:

sample batch file for running GeneMapper® in commandline mode: