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2 hours ago by

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

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