Table 1 Comparison of features of different tools for massive parallel sequencing annotation and interpretation
From: VAReporter: variant reporter for cancer research of massive parallel sequencing
Tool | VARepoter | Vanno [61] | Annotate-it [55] | ANNOVAR [10] | Anntools [62] | KGGSeq [63] | SeqAnt [64] | TREAT [65] | Oncotator [33] |
|---|---|---|---|---|---|---|---|---|---|
Availability | Web | Web | Web | Command line | Command line | Command line | Web | Command line | Both |
Tracking mislabeled specimen | ✓ | ||||||||
SNPs/1000Genomes/COSMIC | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Indels | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Cross-sample comparison | ✓ | ✓ | |||||||
Filters | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||
Domain information | ✓ | ✓ | |||||||
Dynamic summarized chart | ✓ | ✓ | |||||||
Gene Ontology | ✓ | ✓ | ✓ | ✓ | |||||
Mutational Landscape | ✓ | ||||||||
OMIM | ✓ | ✓ | ✓ | ✓ | |||||
Pathway visualization | ✓ | ✓ | ✓ | ✓ | |||||
dbNSFP | ✓ | ✓ | ✓ | ✓ | |||||
Sequence retrieval | ✓ | ✓ | ✓ | ||||||
ICGC/TCGA comparison | ✓ | TCGA only |