Use a new training set

[kantLeroy]

As mentionned in Frequently asked questions section, ClinSV is optimized using a dataset from HiSeq X (and potentially Mechanical Fragmentation library prep). In our lab we move to NovaSeq 6000 / X+ coupled with Tagmentation library prep.

Is that possible to use a new dataset reference to optimize ClinSV with this new lab set up ?
Thanks in advance for any advise.
Q.

[drmjc]

Hi @kantLeroy,
This is a good suggestion, as we too have moved on from HiSeqX to NovaSeq 6000 now to NovaSeq X. The biggest change i'd expect is the the insert size distribution, which is baked into the automated NA12878 validation report. Doing so would also alter the IGV tracks, perhaps smoothing out some SR and DP noise of the coverage stdev tracks.

I think the changes would be pretty modest though, and if it helps alleviate your concerns, this does not stop us from using ClinSV, as is, on 30-40x depth Illumina germline WGS data.

We'd have to re-create the scripts to makes these data, as the developer has left academia, so I don't see it happening in the next quarter. in the backlog to discuss with @J-Bradlee...

cheers, M