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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.