chrgeneticist introduction for reviewer jinlian wang [email protected] 10/8/2014
TRANSCRIPT
https://wangj27.u.hpc.mssm.edu/wes/index.html
2. Click “Run”
1. Download
Download and “Run”
Keep Click ‘Run’
Double click “chrgeneticst.msi” to install the tool_1
Click ‘Next’
Installation path selection_2
You can use the default directory and click”Next”
Installing…
Installing…
Installation done_3
Installed successfully. Click “Close”
After ‘Close’, please check your desktop
Double click the icon to run the tool
Double click the icon
Sign in
User name is Mount Sinai email e.g.
Default password is 9999999 for
everyonePull down the menu and select Reviewer
Click ‘Sign in’
Reviewer Panel
Click and Start reviewing your assignments Your Reviewed
Assignments Browse
Exit
Click this to change your
password
Assignments interface
New assignment
Not completed assignment
Click to start review
If your assignment is not submitted, the status is ‘Modified’
Reviewer’s master table
Save your assignment
Export assignment to
excel
Go Home
Click ‘Next’ to submit your assignment
What does the master table function ?Master table help you to diagnose each variants & make decision based on some evidence.• Check the detailed position information and structure of the variants through
UCSC Genome browser.• Look at the latest publication for each variants• Review the pathogenic information of each variants from HGMD, OMIM,
GeneCard, ClinVar at both gene and variants levels• Provide population frequency information for each variants from ESP6500, 1k
genomes.• Allow you to check the detailed information of each variants though
embedded IGV browser.• Comment with your expertise opinion on each variants.• Auto save the assignments every five minutes• Export your assignments in the format of excel.
Raw column from Ingenuity Variant categoriesClick ‘Transcript
ID’ to IGV
Gene level Variant level Population frequency
Functional impact
Diagnosis Suggestion or
comments
Summary of
comments
Reviewer and Administrator
Function area of the master table
Functions include: 1) sort : click small triangle in the header of each column2) adjust the width of each column same as excel3) freeze column: select the column you want to freeze, right click the header, and put your mouse within the popup window,4) Hide column: same as 3), check the column you want to hide,5) Comments: right click the cell you want to add comments, once the color is blue indicating the cell selected and you can make comments.
Right click the cell to add comments
Right click the header to Freeze/add /remove
columns
Auto save
Mouse over each cell show the out
sourced link
Small icon indicates the
comment made
Click the header to sort each column
Using IGV• After you click the link of “Transcript ID”, IGV
and .bam file of proband will be loaded automatically. In the current version, only proband bam file is included.
• The IGV is running in the server side, so no worries about pre-installation of IGV, only thing is make sure you have installed jdk 7. If you have used IGV before, you don’t need to install jdk 7. If not, please download it from :
• https://wangj27.u.hpc.mssm.edu/wes/index.html
Steps of IGV
IGV launched
If asking for update, check ‘Skip this update’
Submission
Conform your submission
Click ‘Next’ to submit your assignment
Export your assignment to
excel
Exported excel file
Submitted successfully
Submitted successfully, a email will automatically send to administrator
History browse
Click to browse the history
Uninstall from “control panel”
1. Click
2. Click All Programs
3. Control Panel
4. Click “Uninstall a program”
Uninstall chrGenticist
5. Right click “chrGeneticist”
6. Click “Uninstall”
Comments and Feedback
• Please give me your comments and suggestion by email:
• [email protected]• Or call me 202 468 6495 (cell phone)
• Welcome to suggest a good name for this tool