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igv_plotter

python package with scripts for opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc. It includes the following scripts:

  • igv Launches IGV from the command line and optionally makes it load some file(s) and jump to some locus.
  • igv_plotter Automates taking IGV screenshots of one or more data files at one or more loci.
  • igvweb_viewer Allows bam, vcf, and/or bed file tracks to be viewed in a web browser using igv.js.

To install it, run pip install igv_plotter

igv_server

A tool that makes it easy to open remote files on the cluster (bams, vcfs, etc.) in an IGV instance that's running on your laptop.

To set it up:

Run an Apache HTTP server on the cluster (in our case, it's running on a machine called maclab-utils) and have it serve the scripts in igv_server/httpd_server/.

After you set it up:

  • on the cluster, go to the files you want to view and run add_to_igv_server my_file1.bam my_file2.vcf.gz ..
  • on your laptop, open IGV and click File > Load from Server..., then select my_file1.bam and/or my_file2.vcf.gz in the dialog that comes up.