Release note 04.02.18

Folders on the visual interface

We have introduced support for folders on Cavatica. To complement our existing API functionalities, now you can organize your project files into folders throug Cavatica’s visual interface, which allows you to have a better overview of your files and manage them more easily. Some of the currently available options related to folders are the ability to copy and move files between folders, use the optional sidebar tree for browsing, search recursively inside the folder structure and use files from folders as task inputs. In the upcoming period we will be working on adding more options to folders, such as the ability to rename a folder, output task results into a folder and many more.

Uploaders have also undergone some changes in order to add folder support. Two major features are introduced:

  • uploading items (files and/or folders) into folders;
  • preserving folder structure when uploading items.

Both of these features are introduced in CLI and Desktop Uploaders.

Smart Variant Filtering

The variant filtering process consists of selecting highly confident variants and removing the ones that are falsely called. This process used to be mostly left out from deeper testing in secondary genomic DNA analyses, even though it can boost precision of variant calls significantly. After developing graph genome alignment tool and reassembly variant caller, we are now launching the Smart Variant Filtering tool used for filtering germline variants.

Smart Variant Filtering (SVF) uses machine learning algorithms trained on features from the existing Genome In A Bottle (GIAB) variant-called samples (HG001-HG005) to perform variant filtering (classification). The comparison results obtained during deep, three-stage testing demonstrate that it outperforms the solutions currently used within most secondary DNA analyses. Smart Variant Filtering increases the precision of called SNVs (removes false positives) by up to 0.2% while keeping the overall f-score higher by 0.12-0.27% than in existing solutions.

Learn more from our blog post on Smart Variant Filtering and documentation.