Running igvtools from the IGV Interface

Select Tools>Run igvtools to open the igvtools window.  This window allows you to run the toTDF, Count, Sort, and Index tools:

  1. Select the tool that you want from the Command drop-down list.  The toTDF tool is selected by default.
  2. Specify the necessary files and/or genome.
  3. Select any of the alternative options you want.
  4. Click Run.

Information about the run will appear in the Messages box.  Note that if you exit the IGV application, any tool that is in progress will be terminated. 

toTDF

The toTDF tool converts a sorted data input file to a binary tiled data (.tdf) file.  Use this tool to pre-process large datasets for improved IGV performance.

Select:

  • the Input File (supported formats are .wig, .cn, .snp, .igv, and .gct)
  • the Output File (must end in .tdf)
  • the Genome (default is whatever genome is selected in IGV)

Options you can change include:

  • Zoom Levels: specifies the maximum zoom level to precompute.  The default is 7; this is sufficient for most files. This value can be reduced to reduce file size, though it will impair IGV performance.
  • Window Functions: allows user to select the window functions to use when reducing data to precomputed tiles.  Mean is the default, but you can also select Min, Max, or Median, as well as percentiles of the data.
  • Probe to Loci Mapping: specifies a .bed file to be used to map probe identifiers to locations.  This is useful when preprocessing .gct files.  The .bed file should contain 4 columns: chr start end name (where name is the probe name in the .gct file).

Count

Count computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in Chip-seq experiments.  By default, the resulting file will be displayed as a bar chart when loaded into IGV.  To display feature intensity in IGV, the density must be computed with this option, and the resulting file must be named <feature track filename>.tdf.

Select:

  • the Input File, which must be sorted by start position (see the Sort tool, below). Supported file formats are .sam, .bam, .aligned, .psl, .pslx, and .bed.
  • the Output File (must end in .tdf or .wig)
  • the Genome (default is whatever genome is selected in IGV)

Options you can change include:

  • Zoom Levels: specifies the maximum zoom level to precompute.  The default is 7; this is sufficient for most files. This value can be reduced to reduce file size, though it will impair IGV performance.
  • Window Functions: allows user to select the window functions to use when reducing data to precomputed tiles.  Mean is the default, but you can also select Min, Max, or Median, as well as percentiles of the data.
  • Window Size: specifies the window size over which coverage is averaged, in base pairs; default is 25 bp

Index

This command creates an index for an alignment file or a feature file.  Index files are required for loading alignment files into IGV, and can significantly improve performance for large feature files. Note that you do not directly load the index file into IGV. Rather, IGV looks for a corresponding index file when the alignment or feature file is loaded.  This command does not take an output file argument. Instead, the filename is generated by appending ".sai" (for alignments) or ".idx" (for features) to the input filename as IGV relies on this naming convention to find the index . The input file must be sorted by start position (see the Sort tool, below).

NOTE: This tool cannot index a binary (BAM) file.   Use the samtools package to sort and index BAM files.

Select the Input File.  Supported file formats are .sam, .aligned, .vcf, .psl, and .bed.

Sort

Sort sorts the input file by start position.

NOTE:  This option does not work with BAM files.  The samtools package can be used to sort .bam files.

Select:

  • the Input File. Supported file formats: .cn, .igv, .sam, .aligned, .psl, .bed, and .vcf.
  • the Output File

Options you can change include:

  • Temp Directory: specifies a temporary working directory.  For large input files, this directory will be used to store intermediate results of the sort. The default is the user's Temp directory.
  • Max Records: specifies the maximum number of records to keep in memory during the sort.  The default value is 500000.  Increase this number if you receive "too many open files" errors.   Decrease it if you experience "out of memory" errors.