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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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Usage of Sniffles2 for direct RNA sequencing output #517

Open kaltinel opened 3 weeks ago

kaltinel commented 3 weeks ago

Hi,

I hope you are well. I am kindly writing to learn whether it is possible to use Sniffles2 to investigate SVs in direct RNA sequencing data. I have seen in previous issues that there is a related question asked in 2019, but I was unable to see how it proceeded as it seemed like its discussion was taken out offline. If I could use Sniffles2, what would be the required coverage? And, what parameters would you recommend?

Many thanks!

fritzsedlazeck commented 2 weeks ago

Thanks @kaltinel this is indeed very interesting for us too but we have not tested this. In theory it should work,but I would set the min SV size to 1000bp or even more.. This way you avoid the Intron mapping signals and focus on large events (e.g. fusions )only. Hope that helps Fritz