PURPOSE

IGVNavigator (IGVNav) is a tool that was developed to assist in analyzing variants during manual review. Its input is a text file with variant coordinates and its output provides an annotation of these variant coordinates. This annotation includes the call (i.e. somatic, germline, ambiguous, or fail), tags to provide additional information if a variant is called ambiguous or fail, and a notes section for free text

DOWNLOAD

Steps to download IGVNav for Mac:

1) Download IGVNav.zip

2) Unzip File

3) Add unzipped file to Applications/ folder.

INSTRUCTIONS FOR USE

1) Open IGV

2) Load session file (e.g. .bam files)

3) open IGVNav applicaiton

4) IGVNav app will prompt you to open a manual review file.

5) Open a manual review file whereby the format of this file is a TSV file with columns:

Chromosome, Start, Stop, Reference, Variant, Call, Tags, Notes

6) The first six columns (Chromosome, Start, Stop, Reference, and Variant) should be filled-out and the remaining columns will be blank.

NOTE: The column names do not have to match exactly the above, but they do have to be the correct data in the same column order.

7) Navigate through the manual review file using the arrows on the IGVNav interface.

8) Ensure that coordinates on IGVNav interface match the IGV interface.

9) Select a Call for each variant based on support for variant.

10) Select various Tags for each variant if variant is labeled as ambiguous or fail.

11) Input any notes required in the free-text box.

12) Periodically save the manual review file to ensure that calls are recorded. Be sure to save the manual review file prior to closing the IGVNav session.

EXAMPLE INTERFACE

INSTRUCTIONS FOR DEVELOPING

1) clone the repo/ sub-folder

2) Edit IGVNav.py

To build, you will need to install wxPython and py2applet: $ python setup.py py2app

App will be placed in dist/ sub-directory of the repository