Our documentation pages have moved. Please go to https://research-help.genomicsengland.co.uk/ to navigate to the most up-to-date version of this page.
User experience and feedback is critical to maintaining and improving IVA.
Please send any feedback you have to [email protected] with 'IVA feedback' as the subject.
Interactive Variant Analysis (IVA) allows you to query variants and clinical data from participants from the 100,000 Genomes Project using an intuitive web interface. To open IVA, double-click on the desktop application. Then click Login on the top-right of the screen and enter your Research Environment credentials.
Only genomes which have been successfully processed through the Genomics England Interpretation pipeline are included in IVA. We can therefore be confident of the quality and integrity of the clinical and genomic data provided as genomes which fail quality control checks (such as contamination, genetic vs reported checks, coverage etc) are not included. Only small variants are included in IVA - structural variants can be accessed via the raw VCFs.
As a GeCIP or Discovery Forum member, you will be able to query data from four different studies. You will be able to see a breakdown of these studies by clicking on the username tab on the top menu and selecting Projects.
|Project||Study||Description||Genome Assembly||Number of samples||Number of variants||Aligner||Variant caller|
|100k Genomes Project GRCh37 Germline||RD37||Rare disease germline||GRCh37||12,166||289,435,693||Illumina iSAAC||Platypus (0.8.1)|
|100k Genomes Project GRCh38 Germline||RD38||Rare disease germline||GRCh38||33,190||439,334,686||Illumina iSAAC||Platypus (0.8.1)|
|100k Genomes Project GRCh38 Germline||CG38||Cancer germline||GRCh38||9,167||286,136,051||Illumina iSAAC||Starling (2.4.7)|
|100k Genomes Project GRCh38 Somatic||CS38||Cancer somatic||GRCh38||9,589||398,397,146||Illumina iSAAC||Strelka (2.4.7)|
After logging in, click the Studies tab on the top menu to select your study. Be careful to note which study you are currently investigating!
Once you have selected a study, click Variant Browser on the top menu. This browser allows you to view and filter variants for your chosen study using multiple parameters, which can be found in the left-hand menu. The filters available are:
Once you have defined your filters, click Search to show the resulting variants in table format, as in the screenshot below. (Summary format is not yet available.)
Remember to click Clear if you want to clear your applied filters. If you are experiencing issues with filtering, click Clear and re-try.
You can use this table to browse features of these variants, such as variant type, consequence type and population frequency. You can also download the table as a tab-separated values or JSON file.
Click on the row for a particular variant to view additional information on this variant below the table: