Tumor Only Adaptive Sampling

[ziphra]

Hello,

I have tumor only nanopore long read sequencing, from adaptive sampling experiment. Is it worth phasing and happlotaging the bam?
Should I filter the bam for target regions only before running Severus?

Thank you!

[aysegokce]

Hello @ziphra,
Severus requires the full, unfiltered BAM file for optimal performance, as prior filtering can reduce recall.

Phasing does not affect SV calling in tumor-only mode; however, it may still be beneficial if the target regions are long and complex SVs are expected.

Apologies for the late reply, and thank you for your patience.

Best,
Ayse