Are calls made from supplementary alignments?

[jo-mc]

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]

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