Missing caller info for SNVs in cancer-cases (except for VarDict)

[mathiasbio]

Hi guys!

I've been looking a bit into the SNVs uploaded to Scout from the cancer side and I can see that from the TGA cases they have this label "VarDict: PASS" but from the WGS calls made by TNscope there's none.

I've been looking into the VCF to try to understand where it's reading this info of which caller made the call but can't find anything except in the VCF header under "source". For the next release of balsamic we're merging the TNscope and VarDict calls, and I can see from the test case I've uploaded to stage that this caller info is missing there too. Is there something we need to do on our side to get this info into Scout?

Thanks!

[dnil]

Well, we have it for cancer SNVs, either TNscope or TNscope_UMI. Did you specify it with FOUND_IN or SET?

Maybe you could point to a sample VCF and we can take a look?

[mathiasbio]

I see! I needed to search with case-insensitive. But ok! Then I just need to add this FOUND_IN to my merged VCF with the correct callers? Does it matter if I add it as "tnscope" or "TNscope"?

[dnil]

It just might! 😅 The tag should be the lower case version.

[dnil]

But, sounds good, caller tags are coming to these files as well! Closing this for now, right?

[mathiasbio]

Yes! Added to balsamic PR here: Clinical-Genomics/BALSAMIC#1475