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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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Are calls made from supplementary alignments? #502

Open jo-mc opened 3 months ago

jo-mc commented 3 months ago

Hello, I have a alignment with supplementary reads having an insertion. They do not appear to be in the VCF file. I had a quick look over documentation but did not find anything. How does sniffles handle this?

Thanks.

fritzsedlazeck commented 3 months ago

Thanks for brining this up. We will fix it in the next version. This was a performance approach that we did previously and we accidentally kept that. Thanks Fritz