5.20 bedToIgv

bedToIgv creates an IGV (http://www.broadinstitute.org/igv/) batch script (see: http:// www.broadinstitute.org/igv/batch for details) such that a ??snapshot?? will be taken at each features in a feature file. This is useful as an efficient means for quickly collecting images of primary data at several loci for subsequent screening, etc.

NOTE: One must use IGV version 1.5 or higher.

5.20.1 Usage and option summary


bedToIgv [OPTIONS] -i <BED/GFF/VCF> > <igv.batch>
Option Description
-path The full path to which the IGV snapshots should be written. Default: ./
-sess The full path to an existing IGV session file to be loaded prior to taking snapshots. Default is for no session to be loaded and the assumption is that you already have IGV open and loaded with your relevant data prior to running the batch script.
-sort The type of BAM sorting you would like to apply to each image. Valid sorting options: base, position, strand, quality, sample, and readGroup Default is to apply no sorting at all.
-clps Collapse the aligned reads prior to taking a snapshot. Default is to not collapse.
-name Use the “name” field (column 4) for each image’s filename. Default is to use the “chr:start-pos.ext”.
-slop Number of flanking base pairs on the left & right of the image.
-img The type of image to be created. Valid options: png, eps, svg Default is png.

5.20.2 Default behavior


bedToIgv -i data/rmsk.hg18.chr21.bed | head -9
snapshotDirectory ./
goto chr21:9719768-9721892
snapshot chr21:9719768-9721892.png
goto chr21:9721905-9725582
snapshot chr21:9721905-9725582.png
goto chr21:9725582-9725977
snapshot chr21:9725582-9725977.png
goto chr21:9726021-9729309
snapshot chr21:9726021-9729309.png

5.20.3 Using a bedToIgv batch script within IGV.

Once an IGV batch script has been created with bedToIgv, it is simply a matter of running it from within IGV.

For example, first create the batch script:

bedToIgv -i data/rmsk.hg18.chr21.bed > rmsk.igv.batch

Then, open and launch the batch script from within IGV. This will immediately cause IGV to begin taking snapshots of your requested regions.

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