How can I export a full alignment from IGV as an image?

Question

The IGV browser lets you export an alignment as an image (File => Save Image). However, this image only contains those reads that fit in the viewing window:

As you can see in the image above by looking at the scroll bar on the right, this is only a small subset of aligned reads. Is there any way to export an image of the aligned reads that includes all reads and not only those currently shown in the window?

Answer 1

Running an IGV batch script helps increase the number of reads per image, compared with File | Save image, but it does not solve the issue by itself.

To run a script, first make a script file like so with 1 command per line:

snapshotDirectory ./
goto chr2:28582094-28582790
maxPanelHeight 10000
snapshot chr2_28582094_28582790.png

Run the script using Tools | Run batch script menu. The importat trick is the maxPanelHeight 10000 which is what makes this include more reads than the default snapshot.

You can also convert this into a little shell script:

#!/bin/bash
mkdir -p /tmp/igv
sleep 2
echo "snapshotDirectory /tmp/igv"
sleep 2
goto chr2:28582094-28582790
sleep 2
echo "maxPanelHeight 10000"
echo "snapshot chr2_28582094_28582790.png"

Then, just open IGV, load the relevant BAM file and run the script like this to connect to IGV via telnet (credit to Pierre Lindenbaum):

sh foo.sh |  telnet 127.0.0.1 60151