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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
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Nirvana JSON file formats (small variants) documentation #27

Closed pablo-esteban closed 3 years ago

pablo-esteban commented 5 years ago

The json file format documents contain a broken link in the description of the vid field. The description column only contains the text "Illumina Variant IDentifier" that links to https://confluence.illumina.com/display/PAT/VID which results in a page-not-found error.

Both Nirvana JSON file formats (small variants) files (1.5.4 and 1.6.2) in the Output File Formats have this issue (p9 and p7, respectively).

MichaelStromberg commented 3 years ago

Hi Pablo,

Thank you for the update. We're in the process of moving to a new documentation website where we can share that information more readily: https://illumina.github.io/NirvanaDocumentation/

The VID page is not on that site yet, but we'll add it this week.

In essence, our new VIDs are the same as the Broad Style VIDs that you see on the ExAC and gnomAD pages: I.e. 2-1000-A-C is a variant on chr2 position 1000 where A --> C

MichaelStromberg commented 3 years ago

FYI: The new VID page is now up: https://illumina.github.io/NirvanaDocumentation/core-functionality/variant-ids