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