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:
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:
mkdir -p /tmp/igv
echo "snapshotDirectory /tmp/igv"
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