The window size over which coverage is averaged. Specifies the maximum zoom level to precompute. If the output file is named "stdout" the output will be written to the standard output stream in. wig file, list both output filenames as a single string, separated by a comma with no other delimiters. To indicate that you want to output both a. The output filename must end in ".tdf" or ".wig", or be the special string "stdout". OutputFile The output file, which can be binary. By default, the resulting file will be displayed as a bar chart when loaded into IGV. Common usages include computing coverage for alignment files and counting hits in ChIP-seq experiments. The count command computes average feature density over a specified window size across the genome. Attempting to preprocess an unsorted file will result in an error. Files can be sorted with the sort command described below. gct files, must be sorted by start position. Igvtools toTDF -z 5 copyNumberFile.cn copyNumberFile.tdf hg18ĭata file formats, with the exception of. This option is useful when preprocessing. bed file to be used to map probe identifiers to locations. To reduce file size at the expense of IGV performance this value can be reduced.Ī comma delimited list specifying window functions to use when reducing the data to precomputed tiles. The default value is 7 and is sufficient for most files. InputFile The input file (see supported formats above). Note: This tool was previously known as tile Use this command to pre-process large datasets for improved IGV performance. The toTDF command converts a sorted data input file to a binary tiled data (.tdf) file. For example -Xmx1500m requests 1500 MB, -Xmx1g requests 1 gigabyte.įor more information about other settings, see the downloaded file igvtools_readme.txt.
The memory is set via a "-Xmx" parameter. If this happens you will need to edit the scripts to reduce the amount of memory requested, or use the Java startup option. If this is more than the amoount available on your platform, you will get an error along the lines of "Could not start the Virtual Machine". The igvtools scripts allocate a fixed amount of memory. We recommend the shell scripts above for most users. Note that the command line has become more complex with Java 11 compared to Java 8. Java -Xmx1500m -module-path=lib -module=org.igv/.IgvTools gui In the example shown below, igvtools is started with 1500 MB of memory allocated and launched in the location where you have unpacked IGVTools. This option allows more control over Java parameters, such as the maximum memory to allocate. Igvtools can also be started directly using Java. Recognized commands, options, arguments, and file types are described below. The general form of the command-line version is:
Once the GUI version has been launched, the commands and options are the same as when you run igvtools from the IGV interface. Igvtools_gui.bat (GUI version for Windows) Igvtools.bat (command-line version for Windows) Igvtools_gui.command (alternate double-clickable GUI version for MacOS 10.x) Igvtools_gui (GUI version for Linux and MacOS 10.x) Igvtools (command-line version for Linux and MacOS 10.x) The igvtools utilities can be invoked, with or without the graphical user interface (GUI), from one of the following scripts: The igvtools utilities can be downloaded from the Downloads page on the IGV website.