A secure, versatile site for VCF manipulation that runs entirely in the browser.
Website: https://compass.dna.land
GitHub: https://github.com/TeamErlich/dna-land-compass
Compass accepts a matching compressed VCF and Tabix index file. These files must have the extensions .vcf.gz and .vcf.gz.tbi, and they must have the same file name up to ".vcf".
Compass will read the index file in its entirety on the user's computer, and it will scan the compressed VCF upon request. No information from the user's files—at any point—is transmitted or retained, eliminating a category of security vulnerabilities. The user can then search through their files in two ways. They may enter the rsID of an individual SNP, or they may select a topic (e.g., "Crohn's Disease") of interest, which returns SNPs that influence the topic with a p value below a certain threshold.
The site uses the dbSNP database to gather the coordinates (chromosome and position) of each SNP, and NCBI's Phenotype-Genotype Integrator (PheGenI) to connect certain SNPs with physical conditions.
Once the coordinates are used to decompress a section of the user's VCF, the selection of SNPs is returned in a report. For each variant, the genotype is displayed, along with an array of resources (SNPedia, PubMed, dbSNP, GWAS, and Google).
Anyone can download the source files for Compass and even access our back-end. Here's how:
- Download and unzip this repository.
- Open
index.htmlin Safari, Chrome, or Firefox.
That's it!
A manuscript is forthcoming, please stay tuned!
Copyright (C) 2016 Erlich Lab
All rights reserved.
Comapss is released under the BSD license. See the LICENSE file for more information.
Questions and feedback are welcomed and appreciated. Please email us at compass@dna.land.