I am working with sequencing data generated by minion. I used minimap2 to align the long reads to reference human genome GRCh38. Now I want to call SNPs and indels, I have been searching for a tool that can work with bam files generated by minimap2.
1- Is there variant caller that work with fastq files (not fast5) and can work with bam files generated by different aligner?
2- why do the majority of variant calling tools (for nanopore) require bam files that are generated by specific aligner?