1. Python Installation
In order to run ClinTAD locally, you must install Python. ClinTAD was developed using Python version 3.6.4, but most versions of Python 3 should work. When installing Python, please check the box to add Python to PATH.

2. ClinTAD Installation
The code for ClinTAD can be found on Github .

3. Custom Tracks
Click on the Login button on the top right side of the website, create an account if needed, and login. Once you are logged in, click on the settings button at the top right and then click on the Tracks button in the dropdown menu. Fill out the Create New Track form, upload the file with your data, and click submit. The required file format is shown below with examples (columns are separated by tabs):

TADs

Chromosome Number	Start Coordinate	End Coordinate
1	1000000	2000000
1	2000000	3500000

CNVs and Enhancers

Chromosome Number	Start Coordinate	End Coordinate	Element ID, Name, or Label	Element Details
1	1000000	1009000	Element 1	Element 1 is a very important element!
1	2000000	2050000	Element 2	Element 2 is important for gene expression in several tissues!

4. Data Sources
For details about the specific files used in creating the ClinTAD database, please see the ReadMe.md files in the /home/files folder of the GitHub repository. This folder is broken down into subfolders by type of data and source, e.g there is a folder for genes and a folder for Human Phenotype Ontology (hpo) data.

For the code used to read these files into the database, please refer to the /home/management/commands/load.py file.

a. TAD Boundaries
The default TAD boundary file was provided by Jesse Dixon. The boundaries are derived from human embryonic stem cell data described in Chromatin architecture reorganization during stem cell differentiation, using the HG19 genome build, a bin size of 40kb, and a window size of 2Mb.

Other TAD boundaries can be used by logging in and selecting or uploading a different TAD boundary track.

b. Human Phenotype Ontology File
The phenotype file used for this website is a modified version of the hp.obo file from Human Phenotype ontology, which was downloaded on December 2, 2017. Of note, the modified file used for this site is a list of combined ID fields and name fields from the original hp.obo file. Currently, the HPO Phenotype Lookup form only searches for matches between the input string and the hp.obo name field. Searching for matches in the "def" and "comment" field of the hp.obo file may be added in the future.

This tool was developed at the University of California San Francisco by Jacob Spector, MD and Arun Wiita, MD PhD. Please cite:

Spector JD, Wiita AP. ClinTAD: a tool for copy number variant interpretation in the context of topologically associated domains. J Hum Genet. 2019;64(5):437-443. doi:10.1038/s10038-019-0573-9

ClinTAD has an API that is available to registered users. Up to 500 requests per day can be made. Documentation for the API can be found on this page.

Please email us at ClinicalTAD@gmail.com with bugs, suggestions, or questions.

Problem: The Single page is not loading or is causing the browser to crash.
Resolution: This can happen due to invalid inputs into one of the forms. Click the button below to clear the data, then try using the Single page again.

Clear Data

1. Add tracks
    a. CTCF binding sites
    b. CNV depletion (how frequent CNVs are at location)
2. Case Repository
    a. Create a page where users can add interesting cases
3. Machine Learning Model
    a. Determine if machine learning can assist with determining pathogenicity of variants based on phenotype matches