The VarSome API

VarSome's high-performance variant annotation Application Programming Interface (API) makes it possible to annotate variants using data from over 30 genomic databases. You can start your project immediately and without incurring the significant overheads of integrating and maintaining all these feeds yourself.

The API has been designed to be as simple as possible to use: a simple REST API is provided, data requests are returned as JSON. This makes it ideal to integrate into Python, R, Perl, Java, or any other programming language.

A full set of documentation is available here, with simple example queries.

 

A Working Example

We provide a reference API client for Python which demonstrates how to annotate a VCF file. You can simply clone this repository and adapt the code to your own needs.

 

Annotating Whole Exomes or Genomes

The VarSome API has been designed with performance in mind: in practice it can fully annotate over 600 variants / second over an average internet connection. This is made possible through "batching" requests, as demonstrated in the reference API client: each API request can contain several thousand variants in a single call. A user-configurable allele frequency filter allows you to further increase throughput up to 4x faster: this filter will reject variants whose gnomAD allele frequency is higher than a threshold that you set.

 

To set it up

You can already use the VarSome API in a limited fashion (up to 120 queries per hour) if you are logged in on VarSome. For regular access, please look at the plans below and contact us, specifying which plan you wish to subscribe to. We will send you an authentication token that will increase your request limits and enable you to batch several variants in a single request.

 

Feedback

Saphetor is always trying to innovate and make a positive contribution to human genomics, so do please use the Feedback form (bottom left of the screen) to send us feedback & suggestions as to how we can improve our services.

 

Plan Test † Standard Dedicated Server
Variants per month 100,000 unlimited unlimited
Non-variant queries per month 500 unlimited unlimited
ACMG classification      
Option to filter out high frequency variants*      
Get list of variants in genomic region      
Price per megabyte of data**
Minimum per month
0
0
$0.29 / €0.25
$395 / €335
contact us

 

Prices are shown in US dollars / Euros. Pricing in British Pounds and Swiss Francs is also available.

† Queries will only return data for variants in chromosome 17

* If the allele frequency filter is enabled, only variants that pass the filter (ie: those below the given frequency or not present in gnomAD genomes) that require annotating will count toward your monthly variants total. High frequency variants will be ignored. This filter is user configurable, and it will likely reduce the actual number of variants that need to be examined by over 95%, thus enabling fast whole exome or genome analysis.

** Indicative byte output:

Average genomic variant from a real whole genome sample with all data except publication expansion: 2506 bytes (parameters: add-region-databases=1&add-source-databases=all&add-transcripts=all)

Same with filtering out variants with more than 5% allele frequency: 323 bytes (parameters: allele-frequency-threshold=.05&add-region-databases=1&add-source-databases=all&add-transcripts=all)

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