Table 2:

Methods for tandem repeat variant annotation and discovery

Reference annotation
Class of repeat	Method				Reference
STR, VNTR	Repeat Masker				[41]
STR, VNTR	Tandem Repeats Finder				[29]
STR, VNTR	TANTAN				[42]
STR, VNTR	ULTRA				[43]
Satellite	SRF				[52]
Satellite	Repeatnet				[53]
Satellite	Alpha-CENTAURI				[54]
Segmental Duplication	DupMasker				[49]
Segmental Duplication	SEDEF				[50]
Segmental Duplication	BISER				[51]
Variant discovery, short-reads
Class of variant	Method	Size range*	Precision	Untargeted**
STR	RepeatSeq	< RL	exact		[55]
STR	LobSTR	< RL	exact		[56]
STR	hipSTR	< RL	exact		[95]
STR	TREDPARSE	< 500 bp	exact, estimate		[57]
STR	ExpansionHunter	< 1kb	exact, estimate		[60]
STR	exSTRa	Any	estimate		[59]
STR	ExpansionHunter-denovo	Any	estimate	yes	[64]
STR	STRetch	Any	estimate		[62]
STR	STRling	Any	exact, estimate	yes	[63]
STR,VNTR	GangSTR	Any	exact, estimate		[58]
VNTR	adVNTR-NN	Any	estimate		[66]
VNTR	CNVnator	Any	estimate		[67]
VNTR	danbing-tk	Any	estimate		[69]
Variant discovery, long-reads
VNTR	TRViz	< RL	exact		[79]
VNTR/STR	vamos	< RL	exact		[80]

^*Size range <RL are limited to the sample read length.

^**Untargeted methods do not require a list of input tandem repeat loci to analyze.