Variant Browser (BETA)

Variant Browser is under active development with features being added successively. For any suggestions or bug reports, please contact our support team at support@sbgenomics.com.

Variant Browser is an application for genome analysis and interpretation that will allow researchers and clinicians to quickly annotate and accurately prioritize variants and genes involved in a disease. Variant Browser bridges the gap between sequencing/raw data management and clinical management, providing robust genome interpretation to expedite diagnosis and accelerate the understanding of the genetic basis of disease, drug response, and health.

During the BETA stage, you are able to interpret demo VCF files which are readily available inside the app. The available options include filtering with configurable filtering criteria, directly opening the Genome Browser at the position of the selected variant and displaying general statistics for the currently applied filters. In case you want to interpret your own VCF files please contact us at support@sbgenomics.com.

Genome Browser official release

Genome Browser is no longer in the beta stage and has been officially released. The most important achievement in this release is guaranteed accuracy based on manual review of fields in the standard file compared to the most commonly used genome viewer.

Latest additions to Genome Browser also include a history of the last ten positions within the file, easier insertion of markers that takes less clicks than before and the ability to select a different reference file instead of the one that has been preselected based on the headers in the loaded BAM file.

App archiving

We have introduced the option to archive apps that you don't intend to use in a project. Archiving will hide an app from the apps list, workflow editor and other relevant places across the CGC. However, this will not affect reproducibility, as you will be able to rerun existing tasks containing the app.

Multi-Instance Whole Genome Sequencing GATK4.0 Workflow

We’ve published the Multi-Instance Whole Genome Sequencing BWA/GATK 4.0 workflow. This workflow keeps a similar price, with the improvement in total execution time of up to 3.0 times compared to a single-instance implementation. The Multi-Instance Whole Genome Sequencing workflow processes a 30x whole genome in as little time as 3 hours without any additional computational resource such as GPU or FPGA.

Data Cruncher Interactive Analyses - Public project

As a part of the effort to grow a comprehensive set of CGC features and capabilities, we have developed several Data Cruncher Interactive Analyses as an additional resource that should help users mitigate challenges related to interpretation of data obtained through secondary analysis. These Data Cruncher analyses can be found in the Data Cruncher Interactive Analyses public project.

API bulk actions

Due to popular demand, we have created several new API bulk calls. These calls allow users to perform an operation on up to 100 files within a single API call, while using only one API rate limit. This results in significantly faster completion of operations involving a big number of files.

Rabix Composer v1.0 Release

We’ve released the initial version of Rabix Composer (v1.0), which includes significant improvements over the beta version with respect to the development of CWL 1.0 and sbg:draft-2 applications on your local machine.

Set suggested files for workflow inputs

We’ve introduced the option to set files from public projects as suggested for a file input in a workflow. This will allow anyone who runs the workflow to use the suggested files as inputs in a single click, and only have to add the remaining input files manually. Please refer to documentation for more details.

Folders on the visual interface

We have introduced support for folders on the CGC. To complement our existing API functionalities, now you can organize your project files into folders through the CGC's visual interface, which allows you to have a better overview of your files and manage them more easily.

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.

TLS 1.0 and TLS 1.1 no longer supported

We have removed support for TLS 1.0 and TLS 1.1 protocols. The only supported protocol on the CGC and the CGC API is TLS 1.2. If you are using a client that does not support TLS 1.2, please perform an upgrade to continue using the Cancer Genomics Cloud.

EXPORT TO VOLUMES: COPY-ONLY PARAMETER

We've added an Advance Access copy-only parameter to the Start an Export job request for Volumes. This means that, while it is fully operational, it is subject to change. If this parameter, copy_only, is set to true, the specified file will be copied to a volume but the source file will remain on the CGC. Learn more from our documentation.

SUPPORTED INSTANCES UPDATE

We now support the use of new generation AWS EC2 Compute Optimized instances (C5) and General Purpose instances (M5) in task executions and Data Cruncher analyses on the CGC.

DATASETS API UPDATE

The ICGC dataset is now available on the CGC and is queryable via both the Datasets API and the Data Browser.

CASE EXPLORER

The Case Explorer now utilizes TCGA GRCh38. Learn more from our documentation.

TCIA, CPTAC, AND TARGET IN THE DATASETS API

You can now query TCIA, CPTAC, and TARGET data via the Datasets API.

AMAZON KMS SUPPORT FOR VOLUMES

You can now use Amazon KMS with your Amazon S3 volume. Simply provide your KMS ID when configuring your volume for the CGC. Learn more from Amazon's documentation about using a KMS ID.

SEVEN BRIDGES COMMAND LINE INTERFACE

We are rolling out the release of Seven Bridges Command Line Interface (version 0.5.0) which will make our public API accessible through the command line as well.

RABIX BETA RELEASE ON CGC

When you create or edit a tool or workflow on the CGC you’ll see a message asking if you want to try our beta release of Rabix, our new Software Development Kit for the Common Workflow Language (CWL). Rabix consists of two tools.

TCGA GRCH38 DATASET UPDATE

The CGC is committed to providing its users with the most up-to-date version of the TCGA GRCh38 dataset that is available from the NCI Genomic Data Commons (GDC). In keeping with this commitment, the CGC transitioned from hosting version 5.0 of this dataset to version 7.0 on August 17, 2017.

SUPPORT FOR AMAZON WEB SERVICES SPOT INSTANCES

Seven Bridges has introduced support for Spot instances on the Amazon Web Services (AWS) deploy of the Cancer Genomics Cloud. Spot instance support can be selected as a default for projects and and an option for each task execution. By selecting a spot instance execution costs can be dramatically reduced. Our testing indicates an execution cost savings of over 75% on common workflows.

DATASET IMPROVEMENTS

TARGET GRCh38 Dataset

The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) dataset provides genomic, transcriptomic, and epigenomic data from patients representing several childhood cancers and serves as a valuable complement to the existing genomic and multi-omic datasets available on the CGC. The complete TARGET GRCh38 dataset, which includes both Open Data accessible to all researchers and Controlled Data, to which access is regulated by the Database for Genotypes and Phenotypes (dbGaP), is now available on the CGC. This dataset can be queried using the Data Browser to generate custom cohorts from within this dataset as well as cohorts derived from multiple similarly aligned datasets such as the TARGET GRCh38 and TCGA GRCh38 datasets.