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Convert Text File into Marker Map DSM Format

4.2 Convert Text File into Marker Map DSM Format

The process of importing a genetic marker map begins by selecting the Tools > Genetic Marker Maps menu item which brings up the Genetic Marker Map window (see Figure 22). Clicking on the Convert Text File button will bring up the Import Text Marker Map dialog. The Browse button will cause a standard file manager to be displayed so that a file can be selected. The type of delimiter used in the text file needs to be specified for the file format. If a delimiter other than comma, white-space, or tab is used in the file, the delimiter can be specified by selecting “Other ->” in the drop down menu and indicated in the text box to the right of the menu. If the text marker map uses a custom encoding for missing values, that can be specified on the Advanced Options tab.

NOTE:

• Affymetrix marker maps obtained by exporting annotations as a tab-delimited text file from GDAS may have an extra row at the top of the file. Other Affymetrix annotation files could have 15 rows of header information, depending on how they were obtained. These extra rows can be ignored by checking the Skip button on the Advanced Options tab and choosing the number of rows to skip.

After you select OK, the text marker map will be scanned and the Choose Columns to Use dialog will appear. Columns for the marker name, chromosome and position must be specified, and additional columns can be imported from the marker map as well. Clicking OK will convert the text marker map file into a DSM file for use in any project. DSM is a binary format for storing marker map information optimized for use as reference information. If there already exists another marker map by the same name in the Marker Maps folder in the program directory, then a version number will be appended to the marker map file name.