Release notes - August 1, 2022

Annotation Explorer now available as a dedicated app on BioData Catalyst powered by Seven Bridges

Annotation Explorer, otherwise known as TOPMed Annotation Explorer, is now also available as an entirely rewritten, dedicated application in the Data menu on BioData Catalyst powered by Seven Bridges. This makes it more accessible and easier to use compared to TOPMed Annotation Explorer that is run as a Data Studio interactive analysis.

Annotation Explorer enables you to interactively explore, query, and study characteristics of an inventory of annotations obtained using Whole Genome Sequence Annotator software.

This application can be used pre-association testing, to interactively explore aggregation and filtering strategies for variants based on annotations. It can also be used post-association testing to explore annotations associated with set variants, say for example, variant sets found significant during association testing. Currently, annotations for TOPMed Freeze8 variants and Genome wide annotations are integrated with the Annotation Explorer.

Researchers who are approved to access one or more of the TOPMed studies with Freeze8 variant data will have the ability to access the Freeze8 annotation data in the Annotation Explorer. Researchers without access to TOPMed studies can try out the Annotation Explorer with the open access Genome wide annotations for all combinations of SNVs, including each position in the genome as well as INDELs submitted to dbSNP.

To be able to access and use the new Annotation Explorer on BioData Catalyst powered by Seven Bridges, please send a request to our Support team.

Disabled accounts can now be reactivated in a snap

Accounts that are locked or disabled due to inactivity can now be automatically reactivated by their owners. A new, streamlined flow allows you to initialize the process by sending a reactivation email to your email address after logging in with your last used credentials. By clicking the link in the email and setting a new password on the Platform, you will have unrestricted access to your account and data again.

Recently published apps

We have just published and updated our public apps gallery with:

• GATK VariantEval BETA 4.2.5.0, a tool which is used for evaluating variant calls.
• GATK FilterMutectCalls 4.2.5.0, a tool which is used to filter somatic SNVs and indels called by Mutect2.
• Picard CreateSequenceDictionary 2.25.7, a tool for creating a DICT index file for a sequence.
• WARP ExomeGermlineSingleSample 2.4.4, a pipeline for data pre-processing and variant calling in human WES data.