Homozygosity Mapping Service

Homozygosity Mapping is a powerful technique used to narrow the search space for disease-causing variants in exome sequencing data. This has traditionally been performed using a separate micro-array based experiment, but with costs of exomes continuing to fall, homozygosity mapping can be performed using only exome sequence.

This project is the public, anonymous, token-based front end to the analysis tool, which can retain the region containing the disease-causing variant in a consanguineous pedigree, while eliminating XXX% of identified variants from consideration.

You can run the analysis as a web service or a standalone script.

Screenshots

Requirements

Web Service

• A *NIX server with the bash interpreter, openssl, and curl
• unzip, tar, unrar, unrar, and bunzip2
• Python 2.7
• A running MongoDB server
• A running Nginx server

Analysis Tools

• Java 1.7
• Perl
• Genome Analysis Toolkit
• VCFTools
• PLINK
• SAMtools
• BEDtools

Installation & Configuration

Standalone Script

Please see README.md in the scripts folder.

Web Service

1. Run install first. It should take care of most requirements for you.
   Important: If you're using an RHEL-based system, edit line 17 of install and modify the virtualenv command to point at a compiled version of Python 2.7

    virtualenv -p /path/to/python2.7 .
   

2. Modify settings.py to suit your environment.

3. Look at scripts/run.sh to configure paths to the genomic analysis tools required.

   • It's recommended that you download the required analysis tools in scripts/bin/
   • You'll need to place the hg19 reference in scripts/ref/. It should be called hg19.fa.

4. Place a sample VCF file called "sample.vcf" in autozygosity/static/.

5. Go through the configs/ folder for sample cron, logrotate, and nginx configurations.

Once you've taken care of these, you can start the server:

source ./bin/activate	
./start

Unless you've specified otherwise, this will start ten Gunicorn workers, with the parent listening at 127.0.0.1:5000. Stop the server with:

./stop

If you want a Flask server for testing,

./start flask

Finally, it's highly recommended that you set DEBUG = False in settings.py and use Nginx as a reverse proxy to Gunicorn.

To do

• Log error and debug messages
• Write tests
• Better CSS selector-names
• VCF validator
• Progress indicator for URI download

License

(c) Copyright 2013 Nikhil Anand mail@nikhil.io http://nikhil.io, and Adam Deluca adam-deluca@uiowa.edu http://genome.uiowa.edu

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.