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Table 1 Comparison with other web servers features

From: GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases

Feature \ Web servers

PhenIX

eXtasy

OMIM Explorer

Phen-Gen

wAnnovar

GenIO

Year of last update

2014

2013

2016

2013

2015

2017

Simple Input interface

Yes

Yes

No

Yes

Yes

Yes

Acceptance of VCF files

Yes

Yes

Yes

Yes

Yes

Yes

Phenotype (HPO terms)

Yes

Yes

Yes

IDs only

Yes

Yes

Phenotype (OMIM terms)

No

No

Yes

No

Yes

Yes

List of genes of interest to analyze

No

No

Yes

No

No

Yes

Customizable Rareness of the condition

Yes

No

Yes

Yes

Yes

Yes

Fast responsive interface

Yes

Yes

No

Yes

Yes

Yes

No need of extra files to run

Yes

Yes

Yes

No

Yes

Yes

Trio datasets

No

No

No

Yes

No

No

Freeform text input

No

No

Yes

No

No

No

Email notification

No

Yes

No

Yes

Yes

Yes

Dominant and Recessive in single run

Yes

No

Yes

No

Yes

Yes

Can be used by a medical practitioner

Yes

No

Yes

No

Yes

Yes

Output interface with results

Yes

No

Yes

No

Yes

Yes

Simple Output interface

Yes

No

Yes

Yes

ACMG-AMP Classification

No

No

No

No

No

Yes

M-CAP Classification

No

No

No

No

No

Yes

ClinVar Classification

Top 20 only

No

No

No

Yes

Yes

ACMG Secondary findings

No

No

No

No

No

Yes

Full VCF annotation

No

No

No

No

Yes

Yes

Handful set of candidate variants

Yes

No

Yes

Yes

Yes

Yes

Session saving

No

Yes

Yes

Yes

Yes

Yes

Phenotype suggestion

No

No

Yes

No

No

No

Secure server (https)

No

No

No

No

No

Yes

Multi-nucleotide variants

Yes

No

Yes

Yes

Yes

Yes