Variant calling and phasing

Bioinformatics
A summary of variant callers and phasing software
Published

January 3, 2024

Variant callers

  1. Short-read: GATK, VarScan, MuTect, and LoFreq

  2. Long-read: Clair3, DeepVariant

Phasing software

Population-based phasing

Both of these methods need reference panels. The 1000G Phase3 reference panels can be found here.

  1. Beagle

  2. ShapeIT4

Read-based phasing

  1. WhatsHap works well for both short and long reads

  2. HAT is a method for short reads and long-reads