Finding somatic variants....

With the advent of next generation sequencing technologies, sequencing high numbers of cancer genomes has become increasingly cheap. Many algorithms have been developed to detect somatic alterations in these sequences, but their results differ greatly and show little overlap. This is why we have decided to develop Cake - to integrate results from popular variant calling algorithms and provide researchers with a high-confidence set of somatic alterations to take forward for analyses.

 

Why would I use Cake?

Cake is easy to install and run - and is fully configurable!

Out of the tin, it integrates four popular algorithms to call variants with higher accuracy and specificity that outperforms any one of these algorithms alone. It also provides a large array of configurable variant filtering modules, which significantly reduces false somatic variants. Take a closer look [link].

 

And how do I install it?

Cake is implemented in Perl, and we provide a tutorial and detailed instructions for both Unix and Mac users. Download Cake or take a look at the installation guide or the tutorial.