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Serial snapshots with IGV batch

IGV is a very handy tool. Nevertheless, scrolling from one position to another may be fastidious. Second, the bad aspect of this very user-friendly software, is that you can spend hours looking here and there, with at last no backtrack of your discoveries.

Thankfully, IGV can run in batch mode, allowing, for a targeted list of positions, to take screenshots and store the later in a folder. We’ll illustrate in the following with a small example :

Setting up a session

To test our script, we will first download some publicly available data.

#Download a vcf file (on beagle4 website, you may have to change file name according to last release)
wget http://faculty.washington.edu/browning/beagle/test.r1099.vcf.gz
gunzip test.r1099.vcf.gz
#Create an index
igvtools index test.r1099.vcf
#(You can alternatively prefer to use igvtools from igv GUI)
#Launch igv

To check if everything is right, load the vcf file test.r1099.vcf. Then move to positions chr22:20,000,000-20,100,000.


Set everything to your taste, and save the session :  File, save session, you should obtain a xml file.

Running IGV in batch mode

Now, let’s consider you are interested in some particular position. Let’s say we’ve stored several positions of interest in a csv file. Our aim is to create an IGV batch file.

Basically, we’ll have to load the session, set a directory to store the screenshots, and then move from one position to the other. A very crude version could therefore be. (I know : Why csv ? Because a lot of person still use excel 😦 )

#Create a fake positions list
cat >Liste.csv <<EOF

#Create a ss directory
mkdir IMG
#Write the header of the script
cat >Batch.igv <<EOF
load igv_session.xml
snapshotDirectory IMG
#Now parse the csv file
gawk -F ";" -v R=10000 '{print "goto "$1":"$2 -R"-"$2 + R"\nsnapshot Screen"NR".png"}END{print "exit"}' Liste.csv >>Batch.igv

From, igv, go to Tools, Run a batch script. Load Batch.igv, when all the process will be done, IGV will terminate and you’ll find your screenshots in IMG.

For an even more automated version you can use the script “PrepIgvBatch.sh” available in the scriptotheque

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