Hello, in LongPhase paper, you utilized minimap2 to align sequences to reference, and then performed variants calling using PEPPER-WhatsHap-DeepVariant pipeline. However, to my understanding, when applying minimap2, the output file format is .sam, but the input of variant calling pipeline is .bam. Therefore, it is necessary to utilize samtools toolkit to transfer .sam format to .bam format.
When using samtools, a parameter (-F or -f) named flag is used to filter some unnecessary mapping results. I am not sure how to set flag in long reads, so I ask for your help about your parameter settings in LongPhase. Thanks very much.