tu1026 / igv_exploer

Windows compiled exe download here:

https://github.com/Tu1026/igv_exploer/blob/pyqt/dist/IGV%20Tindel.exe

Build Code

pyinstaller --name "IGV Tindel" -F --icon=APP.ico --add-data="APP.ico;." --add-data="APPICON.png;." --noconsole viewer.py

Usage (Please read VERY CARFULLY )

Please note that the screeshots must be named with this convention chorm.position.gene.sample.mutantReads.png

The betastasis file must have the mutant reads contain in the format of (123) or 0:123:0::0

A current known bug is you cannot undo curation on the first image. I will find some time to implement the fix

Setup:

• Open up the application
• Select folder option on the top left corner and select option "select screenshot folder". You will ger prompted to select the folder where all the igv screenshots are located.
• (optional for first time) You will get asked if you want to load previous progress, ignore if the first time using app.
• Select the file option at the top left and select the "select betastasis TSV" you will get prompted to select the betastsis TSV that is exported for the webpage. Remember to show all silent genes before you export TSV from betastsis

You are ready to start curating the mutations!

Curation:

Control:

• press q to blacklist a gene
• press e to whitelist a gene
• press w to doubt a gene (all the doubted screeshots will be stored in one file so you can review all of them later)
• press b to go back (undo what you just did, you have unlimited undos meaning you can go all the way back to first screenshot)

Output: A results folder will be created in the same directory that the app is in.

Inside the folder you will have three files.

• Blacklist file is the standard format that betastasis uses so you can upload this to tambio and let the machine do the blacklisting.

• CuratedFile has all the records of all the screeshot so you can see if something has bee curated, blacklisted or doubted.

• Finally, you have the checklist, which contains all the screenshots that you doubted so you will need to review these.

igv_exploer's Issues

Adding Flags for blacklisting

Recently we have had a discussion about keeping track of why things are blacklisted. Might be nice to store that some way

Move away from using server tables

• Use the vcf tables instead
• Add curation status within the vcf tables and make it as an output