I am currently working on nanopore reads, and trying to calculate the SNP and Indel count. I mapped the reads with Minimap2. From here I called the variants with GATK.
I know that GATK is actually written for short Illumina reads, so I was wondering if the results from the variant calling are trustworthy and whether there is a tool which is specialized on calling variants based on nanopore reads.
Thank you for your help