Call large indel with small genomes #577
Description
Hi,
Thank you all for making this amazing caller!
Is there anyone trying to apply Sniffle2 for virus SV calling?
E.g., we focus on the influenza virus and large internal deletions; its genome is relatively small (13 kb, 8 chromosomes).
Typically, sequencing depth is 200x (could reach 10^3-5 depth). However, the overall frequency of reads carrying deletion fluctuates from ~1% to 99% (similar to somatic mutation?), and individual SVs exhibit extensive breakpoint heterogeneity (e.g., >100 deletion types per chromosome, with their breakpoints clustered around a ~100-200 bp region). A schematic graph of breakpoints detected with NGS is shown below (PMID: 38407436).
Considering the high error rate of ONT reads, do you think it's possible to call the breakpoints confidently with sniffles2?
Given this complexity, I suspect adjustments may be needed for bin size and minimum read support thresholds. Do you have recommended settings for such cases?
Thank you so much for your suggestions.
Best regards