Showing posts from October, 2017

Login Changes: Australian Access Federation integration

We've recently changed our authentication to use the Australian Access Federation. The main benefit is that users from other universities across Australia can use their own institutional credentials to access our database, without having to create a new username/password. However, we still have support for generic username and passwords to support our friends overseas. The other benefit of making this switch is to provide a better user experience in terms of data integration from our ecosystem of databases via single-sign on. We can seamlessly pull information from various places to provide an aggregated view of data. Australian users should use the [Login via AAF] option, while others should use [Basic Login].

IGV viewer for whole family

Our first release of the IGV viewer only allowed a single individual to be displayed at a time, with a single VCF and single BAM file loaded up. With the latest release, IGV viewer now loads all family members.

SNP Validation

The process of sequencing and analysis goes through a series of steps with much human involvement, and therefore is prone to error. In order to verify that a patient indeed does have particular variant, we can go through a step of SNP Validation for a batch of patients. We've created a tool that can be invoked through our web portal to determine the smallest combination of SNPs required to uniquely identify a patient within a batch for a predefined SNP panel. This process requires that the BAM file be available and can take a while, depending on the size of the batch.

Chinese frequencies

Displays the frequency of a variant in the Chinese population using our own Chinese healthy controls database. Currently only supports SNVs. INDELS & Structural Variants UNSUPPORTED (at this stage) and will show 0%

Coverage reports available

The sequencing and variant calling process can sometimes be selective in the regions covered in the genome. Therefore it's also important to know about what regions were not well covered to consider false negatives. These coverage reports are now included as part of the 'summary report' downloads. Look for the file names with 'exonReport'.

On-demand recent annotations

At the push of a button, users can request for the retrieval of the most recent annotations for a variant from Ensembl VEP. This is used to supplement the annotations provided by the pipeline which may not be completely up-to-date with regards to it's source of information. Some of the new annotations include things like Clinical significance, Pub med ID and links, Mutation Taster predictions, rsNumbers and much more ... Because of it's dynamic nature, unfortunately these annotations are NOT searchable, but are there to supplement the annotations from the pipeline.

Restore BAMs files

BAMs files are difficult to manage because of their large size. We've employed a new technique that will conserve the use of expensive disk space by pushing BAM files onto archived tape drives. However, that doesn't mean you can't retrieve them. We've devised a clever way to automatically restore archived BAM files at the will of your command through the web portal. Simply click on the 'Restore from archive' link when viewing a variant. Users will get an automated email to notify them that the BAM file has been restored and ready for download or IGV viewing.