Nanopore multisample variant calling

Question

[colindaven]

Dear community,

does anyone know of a nanopore variant caller which can perform multisample (not single sample) SNV calling on long reads (similar to eg Freebayes for short reads) ?

I know of longshot, clair3, Nanocaller, PEPPER etc but haven't seen one which can do true multisample calling, which has advantages vs single sample calling + VCF merging.

Thanks.

[emilydolivo97]

hello colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset

[colindaven]

There was some discussion with others here https://github.com/WGLab/NanoCaller/issues/21, but I never found an adequate solution - actually I did not try at the time and have not worked on ONT SNP calling since. So maybe one of those approaches will work for you.