WGS to cytosure from balsamic?

[heronikdin]

Hi!

As the title says, is it possible to upload WGS samples that are run through balsamic onto cytosure? I have seen that there is this filedownload on the rare disease site for CGH files.

Hälsningar Hero

[dnil]

Sure, a somewhat simple matter of running vcf2cytosure on them! More specifically what features are you interested in? The current setup for RD is converting a set of SV calls (del/dup over a certain size) and showing TIDDIT coverage data. I suppose this will not be very interesting for panels, and likely not for exomes, so I take it we are talking wgs samples? I'll transfer the issue to Balsamic, as the most roadwork will happen there - if a .cgh file is supplied to Scout for the cases, we can easily show it also for cancer.

[hassanfa]

I think this is more of a BALSAMIC issue to generate a CGH file first. Please transfer it Daniel, or can I also do that?

[hassanfa]

Aah you already did! 👏🏽

[heronikdin]

Thank you for the fast reply! The only addtional thing we would like to "see" maybe is somewhat VAF on cytoure, but I am not sure how feasible it is? Other than that, it should not differ more than from the rare disease site. :)

[dnil]

Right, that would take a little fiddling with vcf2cytosure and e.g. TIDDIT, but likely doable. When we discussed that for RD, it got stuck on having good examples. If you have example CGH files with e.g. a B-allele track in it from an SNP array, I would be interested in it for reference!

[heronikdin]

sorry, dont have any of that...

[dnil]

Ping @khurrammaqbool and @ashwini06; we've wrapped the CNVkit and hg38 updates to vcf2cytosure in a new release: https://github.com/NBISweden/vcf2cytosure/releases/tag/0.7.1.

[ashwini06]

From BALSAMIC version 10.0, cytosure files for WGS cases are delivered to the customer. Done in #947