GMT Tutorial Exercise 25

Bin SNP markers

SNPBINNER groups a list of SNP markers into "bins" that can be multiplexed in FlexMAP microsphere-based oligonucleotide ligation assays (OLA) or allele-specific primer extension (ASPE) on the Luminex platform. Please refer to the GMT manual section on SNPBINNER for details.

1. Select BINNER and then SNP UPLOAD.
2. Click Browse and select the file to be imported ("BINNER_SNP_UPLOAD_input_file_example.txt", downloaded in Exercise 3).
3. Select the Marker Set where allele size ranges for the markers to be binned are stored (SNP Markers (MPBCRC:public:mhayden)).
4. Click Upload.
   • The SNPBINNER output lists all the markers that can be analysed together with the same "bin number", shown in the first column of the output.
   • Note the "bin sizes", i.e. the number of lines starting with the same bin number. If bins of a specific bin size are desired, this can be entered as a number in the Bin size text box. SNPBINNER will attempt to create bins of that size, while ensuring that binning restrictions (as descrbed in the SNPBINNER manual section) are applied. Currently, the biggest possible bin size is "12".

An example of a SNPBINNER output file.