Task

Tool

Function

Reference

Alignment

pbmm2 / minimap2

HiFi-tuned long-read alignment

SNV/Indel calling

DeepVariant (HiFi model)

Deep-learning small-variant caller

Phasing

HiPhase

Read-based haplotype phasing

PacBio

SV calling

Sniffles2 / pbsv

Structural variant detection (incl. mosaic)

Tandem repeats

TRGT / TRGT-denovo

Repeat sizing + methylation + de novo

Paralogues

Paraphase

Segmental duplication resolution

Pharmacogenomics

StarPhase / Pangu / PharmCAT

PGx diplotypes + HLA + CYP2D6

Methylation

modkit / methbat

5mC/6mA calling and analysis

PacBio/community

Pangenome calling

vg giraffe / PanGenie / Minigraph-Cactus

Pangenome-aware variant calling

Variant interpretation

Exomiser / LIRICAL / AMELIE

HPO-driven prioritization