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Table 1 Comparison of features of different tools for next-generation sequencing annotation and interpretation

From: Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

 

ANNOVAR

TREAT

VAAST

VarSifter

Var-MD

KGGSeq

SVA

Anntools

VarioWatch

SeqAnt

Annotate-it

Interface

Command line

Command line

Command line

Graphical

Python script

Command line

Graphical

Command line

Web

Web

Web

Indels

x

x

x

x

 

x

x

x

 

x

 

SNPs

x

x

x

x

x

x

x

x

x

x

x

miRNA annotation

x

      

x

  

x

Regulatory region annotation

x

x

   

x

 

x

   

Custom annotation

x

     

x

x

   

Gene annotation

x

x

   

x

x

x

x

x

x

Conservation scores

x

x

   

x

   

x

x

LRT

x

    

x

    

x

MutationTaster

x

    

x

    

x

Polyphen2

x

x

   

x

    

x

SIFT

x

x

   

x

  

x

 

x

Aggregate scores

     

x

    

x

Haploinsufficiency prediction

          

x

OMIM

 

x

    

x

 

x

 

x

NHLBI Exomes

x

         

x

200 Danish Exomes

          

x

1000 Genomes

x

x

   

x

x

x

x

x

x

dbSNP

x

x

   

x

x

x

x

x

x

Gene prioritization

          

x

Literature retrieval

     

x

  

x

 

x

Gene ontology

      

x

 

x

 

x

PPI/complexes

     

x

    

x

Pathway information

 

x

   

x

x

 

x

 

x

Gene expression

 

x

        

x

Statistical analysis

  

x

   

x

   

x

Filter

x

x

 

x

x

x

x

   

x

Complex filtering rules

   

x

 

x

x

   

x

Cross-sample querying

   

x

x

x

x

   

x

Genetic inheritance models

  

x

x

x

x

x

  

x

x

Data sharing

          

x

Visualizations

 

x

    

x

 

x

x

x

  1. OMIM, Online Mendelian Inheritance in Man; PPI, protein-protein interaction.
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Genome Medicine

ISSN: 1756-994X

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