How to get automated screen shots from IGV

1. Run generateBatchFile.py

   !!!! IGV requires that all file paths be full. So when running on a mac start from /Users/...

   python generateBatchFile.py <sample_loc> <vcfFile_loc> <snapShot_loc> <batchFile_loc>

    <sample_loc> Must be the path to a directory containing the .bam & .bai files of the samples you wish to load
   
    <vcfFile_loc> A .vcf file with the locations you wish to take screen shots of
   
    <snapShot_loc> Where you want the screen shots to be saved to
   
    <batchFile_loc> The location to write the igv batch file generated from the preceding information
   

2. Run the batch file in IGV

   • Open IGV & load reference
   • From the menu bar click "Tools --> Run Batch Script..." & navigate to the .txt file generated by generateBatchFile.py

Example: python generateBatchFile.py /Volumes/external/spirodelaBam/ /Users/Daniel/Documents/spirodela/data/CC3-3/vcfFiles/CC3-3_f10.vcf /Users/Daniel/Documents/spirodela/data/ /Users/Daniel/Documents/igvAuto/igvCommands.bat

Then run igvCommands.bat in IGV