From: Steve Chervitz <schervitz@personalis.com>
Date: Friday, February 20, 2015 at 9:41 PM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu>, Loraine Lab <nfreese@uncc.edu>
Subject: Re: letter of support for IGB - Feb 23

Hi Ann & Nowlan,

Just letting you know that I should have my letter of support ready for you on Mon (2/23). I'm running it by my supervisors for approval now.

Btw, I have some questions for you regarding the script interface to IGB:
https://wiki.transvar.org/display/igbman/Scripting+and+the+IGB+command+language

What I'd like to be able to do programmatically is to:

• load multiple BAM files for a given chromosome;
• zoom to a particular region and load data for that region for all BAM tracks;
• create read depth graphs for each BAM file track;
• ensure the graphs are using the same Y-axis range; (for comparability across tracks)
• set the foreground color for a specific track (nice to have!);
• turn off display of the BAM file tracks (to show only the depth graphs + gene annotation track);
• generate an image file of the main display.

Can you let me know if this sort of control is possible using IGB's command language? It would be quite useful!

Thanks,
Steve