If you're working with HiFi data, I'd recommend checking out our variant calling pipeline. It runs variant calling (SNV, INDEL, SVs, and tandem repeats) and phasing (HiPhase).

https://github.com/PacificBiosciences/HiFi-human-WGS-WDL

HiFi SNV calling has exceptional performance (https://www.pacb.com/wp-content/uploads/Application-brief-Comprehensive-human-genomic-variant-detection-with-HiFi-long-read-sequencing.pdf)

When you have long reads the phasing information becomes more valuable than just straight up SNP calling.

There are many tools for SNP calling but fewer for phasing these variants.

Here are some papers that are a good start in my opinion:

• Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing, Nature Communications, 2019
• Long-read reconstruction of many diverse haplotypes with devider Genome Res. 2025

Study the references for these for more alternatives.