Closed waltergallegog closed 4 weeks ago
Hi there,
Thanks for your detailed issue and apologies on my late response! We've updated SAVANA in the latest release to improve our performance and also reported our results on the Valle-Inclan benchmark in our recent preprint. I hope that answers your question - happy to discuss further if you are still seeing variants which aren't reported despite high support.
Many thanks, Hillary
Hello, I was wondering if you have evaluated / trained SAVANA on the Valle-Inclan benchmark. https://www.sciencedirect.com/science/article/pii/S2666979X22000726
From my side, I have checked the deletions, and it seems SAVANA is losing 6 of them from the truth set, in the classification step, when using the default classifier (
classified.sv_breakpoints.somatic.vcf
).Instead if I use
aligned.sv_breakpoints.vcf
and filter it, I get the deletions. 4 of the deletions have good support for TUMOR and 0 for NORMAL.Maybe I'm missing some configuration to make the default classifier work better?
Here is a summary of the six deletions:
These are the deletions from the
aligned.sv_breakpoints.vcf
file:Let me know if I some of the savana output files may be useful.
BR Walter