Load Trio Data into IGV.
This is a short script that slices bams at a provided set of coordinates and then loads them into IGV interactively. The script then pauses for user input with a prompt on the quality of the site. Depending on user input after running, the script either dumps all variant (with coordinate and proband name) qualities to STDOUT or a provided user file.
| Option | Description | Default |
|---|---|---|
| -bams | input of bam paths and variant coordinates (see example_bams.txt) | none |
| -hostname | ip address or hostname of computer on which remote IGV is running | none |
| -port | port number set within IGV to accept data | 60151 |
| -window | window size to slice bams and view in IGV | 50 |
| -slicedir | directory where bam slices are stored | none |
| -volumes | directory where bam slices are stored on local machine | none |
| -output | file to write results to. Default writes to STDOUT. | none |
| -irods | enable irods support. You currently cannot mix irods and non-irods bam in the same -bams input file. | false |
Note: -slicedir and -volumes are seperate so that if bams and slices are stored on a remote machine, you can provide a different directory to store slices and a different directory to view from. On macos, this is typically done via mounting a fileshare which will appear in the /Volumes/ directory.
Note: If providing a file for -output IGVEugene will print results to this file as annotation is entered. IGVEugene will not clobber a file that is already present and will not run. Please either move the old file or use a different file name.
This script takes a file (provided via -bams) in the following column format:
| Column # | Description |
|---|---|
| 1 | Proband bam path |
| 2 | Mum bam path |
| 3 | Dad bam path |
| 4 | variant chromosome |
| 5 | variant position |
| 6 - n | Additional columns of information, will be printed at each site with label Dat[Col#] |
Columns 2 OR 3 can be blank in the form of a '-' to represent no proband/non trio samples.
-
Open IGV and ensure port information is set (go to View->Preferences->Enable Port) to either 60151 or whatever value is in that box.
-
Run trio_slicer:
./trio_slicer.pl -bams <BAMFILE> -hostname <192.168.0.1> -slicedir /scratch/bamslices/ -volumes /Volumes/bamslices/
- Look at bams. The script will proceed one line at a time and pause with the prompt "Site Quality: " and wait for the user to put in some value, or simply press the "RETURN" key. Or, if "QUIT" is entered, all previous variant site information will be dumped for the user.
To use IGVEugene with iRODs (e.g. with the -irods flag), you must meet the following requirements:
- Have a version of samtools installed with irods support and in your path.
- Initialize your access to your iRODs directory (e.g.
kinit). - Have access to the iRODs group that you need to access bams from.
Warning: IGVEugene will not tell you if you meet these requirements! It will just crash with an input/output error or claim that samtools does not support iRODs.