Calling low frequency structural variants from Nanopore amplicon reads

Question

[bioanyimima]

Hello,

I have amplicon sequences obtained from Nanopore sequencing. I got an 'aligned.bam' file using minimap2. The samples consist of a mix of mosaic mutations, so I expect different alleles to show up. Thus, I am looking for software that will call structural variants (mainly indels >10bp), some will be rare and others more common. The end goal is to plot the variants compare to the WT and get their frequency. Suggestions?

Thanks!

Answer 1

[leonardo.caserta]

I would suggest: Nanocaller (easy to use) Clair3 (well recommended) Longshot

And I've just found a paper describing Variabel, I haven't tested yet, but it looks promising

Answer 2

[colindaven]

As you mention structural variants, the current best tool seems to by CuteSV https://github.com/tjiangHIT/cuteSV as recommended by nanopore.

Others include sniffles and more. https://github.com/fritzsedlazeck/Sniffles

I haven't used these for amplicons though, and they might not work well there.