Table 3.

List of UMI-based somatic and germline SNV callers sorted in alphabetical order. For each variant caller, the types of variants that are reported (column 2), whether a complete workflow including UMI handling (extraction, consensus, clustering), read processing, and mapping/alignment is provided (column 3), whether duplex sequencing data are supported (column 4), the library preparation and sequencing protocol companion to the caller (column 5), and the detection of limit reported in the original publication (column 6) are presented. The variant callers and their core algorithms are explained in detail in Section 5.

Variant caller	Type of variant	Complete workflow	Duplex sequencing data	Companion protocol	Detection limit (original paper)
DeepSNVMiner [73]	SNV, indel	Yes	No	Unspecified	0.1%
iDES [72]	SNV, indel	Yes	Yes	CARP-Seq	0.00025–0.025%
MAGERI [74]	SNV, indel	Yes	Yes	Multiple protocols	0.1%
smCounter [49]	SNV, indel	No	No	QIAseq targeted DNA-seq	1%