Coming to SVS: LiftOver Capability

         July 23, 2020

The world has been making a shift to use GRCh38 human genome reference coordinates, but the transition has not been fast. Many of the mainstay human catalog projects are changing to use native GRCh38 catalogs, or are remapping their current data to GRCh38 coordinates. While this seems to be the advancing goal, it is leaving researchers and analysts with the issue of trying to utilize and combine data from GRCh37 (or hg 19), GRCh38 (or hg38), and even GRCh36 (or hg18) human genome references. Golden Helix’s SNP and Variation Suite (SVS) seeks to help by providing LiftOver support in its next release.

LiftOver Support

LiftOver is the ability to convert genome assembly mappings from one human genome coordinate system to another. This can be an issue when raw data is provided from different coordinate systems, or in the case where an annotation source is in a different coordinate system from the source data. All of these conflicting situations can now be handled with SVS.

LiftOver on Import

Lifting over a track on import can be performed by using the Import Variant Sources wizard and selecting the Liftover option on the final screen (the example below is lifting over GRCh38 data to work in a GRCh37 project).

The final import screen then displays the project defined assembly on the top and then allows the user to select which assembly coordinate system to which the input data was aligned. And after selecting Finished the input liftover is complete and the track can be used in its new coordinate system.

LiftOver Any Which Way

LiftOver in SVS is not just limited to data input! The Convert Wizard can be used to liftover any supporting or annotation sources. Again, this is performed on the last screen of the Convert Wizard where the user confirms the starting genome reference assembly, and selects the new assembly to which the track will be lifted over.

We are excited to present this new feature for users to explore in their biomarker analyses!

If you are interested in trialing LiftOver with SVS in the next release, please request a demo, and our team will get you up and running to try it out!

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