d-cole / igvAuto

Contains files to automate genomic viewing using Integrated Genomics Viewer

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