Table 1. Examples of tools which have functions for annotating the sequence context of genomic variants, including breakpoint ambiguity, flanking bases of genomic variants, wildtype/mutated sequences, HGVS nomenclature, nearby variants and short tandem repeats (STR).

Note that primary functions of the listed tools may not be specifically designed for annotating sequence context of genomic variants. Many listed tools also have diverse functions on other aspects.

Tools	Breakpoint ambiguity	Variant flanking bases	Wildtype/mutated DNA sequences	HGVS	Nearby variant	STR	Additional information
VarSCAT	X	X	X	DNA level only	X	X	Variant sequence annotation tool
Tandem Repeat Finder [32]						X	Annotate STRs in FASTA
RepeatMasker [33]						X	Annotate STRs in FASTA
Krait [35]						X	Annotate STRs in FASTA
HipSTR [38]						X	STR calling tool for NGS
STRetch [39]						X	STR expansion calling tool for NGS
GangSTR [40]						X	STR calling tool for NGS
GATK TandemRepeat [37]						X	Annotate variants as STRs in VCF
UPS-indel [26]	X						Annotate breakpoint ambiguity in VCF
SeqTailor [41]			X				Extract wildtype/mutated sequences with VCF and FASTA
Variant tools [42]		X	Wildtype only				A tool for manipulation, annotation, and analysis of genomic variants
VariantValidtor [43]				X			A tool for validation, mapping and formatting of sequence variants