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Calling low frequency structural variants from Nanopore amplicon reads

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!

structural caller variation amplicon nanopore
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updated by colindaven colindaven • written by bioanyimima • bioanyimima

2 answers

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

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written by leonardo.caserta • leonardo.caserta

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.

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written by colindaven colindaven

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