The VarSome API

VarSome's high-performance variant annotation Application Programming Interface (API) makes it possible to annotate variants using data from over 70 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

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.



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 Free contact us contact us


Prices are available in US dollars, Euros and Swiss Francs.

You can cancel your subscription at any time. For the Standard plan, a minimum monthly fee is charged on the first day of each month and it is due for the month in which you cancel your subscription.

† Queries will only return data for variants in chromosome 17. For the Test plan, we are going to cancel your subscription if you do not use the service for three consecutive months.

* 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 be annotated. 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% (depending on the threshold you use), thus enabling fast whole exome or genome analysis.