Hiphase

Description

hiphase website  

HiPhase will phase variant calls made from PacBio HiFi datasets. Key features relative to other phasing tools include:

• Joint phasing of small variants and structural variants
• Support for multi-allelic variation
• Creates longer, correct phase blocks relative to the current best practice
• No downsampling of the data
• Novel algorithms: dual-mode allele assignment and core A* phasing algorithm
• Quality of life additions: innate multi-threading, simultaneous haplotagging and statistics generation

Environment Modules

Run module spider hiphase to find out what environment modules are available for this application.

System Variables

• HPC_HIPHASE_DIR - installation directory
• HPC_HIPHASE_BIN - executable directory

Citation

If you publish research that uses hiphase you have to cite it as follows:

Holt, J. M., Saunders, C. T., Rowell, W. J., Kronenberg, Z., Wenger, A. M., & Eberle, M. (2024). HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. Bioinformatics, btae042.