Table 1.

Selection of phenotype-aware variant prioritisation (VP) software tools based on five suitability criteria ^a

VP software tool	Directly accepting VCF files	Accepting HPO terms	Last updated or published since 2018	Freely available	Local, programmatic access	Refs
Exomiserb	√	√	√	√	√	[8]
LIRICALb	√	√	√	√	√	[35]
VARPPb	√	√	√	√	√	[11]
Xrareb	√	√	√	√	√	[30]
Phenoxomeb	√	√	√	√	√	[42]
DeepPVPb	√	√	√	√	√	[16]
PhenIXb	√	√	√	√	√	[44]
VINYL		√	√	√	√	[18]
eDiva		√	√	√	√	[15]
VarSight		√	√	√	√	[20]
AMELIE	√	√	√	√	No local installation	[14]
GeneTerpret	√	√	√	√	Web-based only	[32]
PhenoPro	√	√	√	√	Web-based only	[31]
MutationDistiller	√	√	√	√	Web-based only	[22]
GenIO	√	√	√	√	Web-based only	[28]
PhenoVar	√	√	√	√	Web-based only	[40]
GEM	√	√	√	Commercial	Web-based only	[3]
EVIDENCE	√	√	√	Commercial	Web-based only	[36]
VarElect	√	√	√	Commercial	Web-based only	[39]
Phevor (now Phevor2)		√	√	√	Web-based only	[38]
Moon	√	√	√	Commercial	Code available on request	[34]
wAnnovar	√	√		√	Web-based only	[43]
OVA	√	√		√	Web-based only	[12]
BierApp	√	√		√	Web-based only	[10]
OMIM Explorer	√	√		√	Broken web link	[25]
QueryOR	√	√		√	Web-based only	[13]
eXtasy	√	√		√	√	[37]
Phen-Gen	√	√		√	√	[26]
PVP	√	√		√	√	[17]
VCF.Filter	√			√	App-based only	[33]
wKGGSeq	√			√	Web-based only	[29]
VAAST	√			Commercial	Web-based only	[27]
VPOT	√		√	√	√	[24]
Ensembl Variant Effect Predictor	√		√	√	No local installation	[23]
Clin.iobio	√	√	√	√	Web-based only	[41]
VarFish	√	√	√	√	Web-based only	[21]
VarAFT	√	√	√	√	App-based only	[19]

^aA grey cell indicates that the corresponding feature is not present.

^bFollowing the completion of a literature review, seven viable VP software tool candidates that met all five suitability criteria (i.e., directly accepting VCF files; accepting HPO terms; last updated or published since 2018; freely available; with local, programmatic access) were selected for testing and comparison.