0.Introduction

VAReporter is a free web-server package designed to support all kinds of disease-targeted sequencing tests for the two dominant sequencing platforms (Ion PGM and Illumina), ranging from single gene tests to whole-exome sequencing tests. VAReporter can provide comprehensive annotation by integrating a wide variety of biomedical databases. Comparison of gene mutation spectrum between study cohorts and TCGA/ICGC tumors is also supported by VAReporter. Moreover, state-of-arts algorithms that take mutation phenotype into account are used to rank the importance of mutated genes. In brief, VAReporter is designed to meet the requirements from individual diagnosis test as well as large-scale research cohort.

The main features of VAReporter include:

  • Quality Assessment & Quality Control for Variant Call Format (VCF) files
  • Genetic variant annotation by local indexed biomedical databases
    • GENCODE Release 19 (GRCh37.p13)
    • RefSeq
    • NCBI dbSNP build 142
    • ClinVar
    • 1000 Genome phase3
      • American
      • African
      • European
      • East Asian
      • South Asian
    • COSMIC
    • The Cancer Gene Census
    • dbNSFP v2.4
    • UniProt
    • Pfam
    • InterPro
    • Gene Ontology & KEGG pathway
    • TCGA Somatic Mutations
    • ICGC Simple Somatic Mutations
    • Cancer Cell Line Encyclopedia (CCLE) Mutation Data
  • Functional Effect Annotation & Prediction
    • MuSigCV (Predition of Gene Mutation Significance)
    • SIFT (Predict effects of nonsynonymous/missense variants)
    • MutationTaster (Evaluation of disease-causing poteintial of sequence alterations)
    • MutationAssessor (Funtional impact of protein mutations)
    • PhyloP (Conservation score of mutation site based on MSA of 100 vertebrate genomes)
  • Mining clinically actionable drug targets
    • DrugBank
  • Visual Analytics Modules
    • Scatter Plot (VCF allele-frequency correlation plot)
    • Dynamic Charts (Google Chart API) & Dynamic Tables (JavaScript library DataTables)
    • Web Interface & Custom Filters (R Shiny)
    • CoMut Plot (Rendering Mutational Landscape from Study Cohort)
    • lollipop Plot (Displaying Mutational Spectrum in specific gene)
    • Pathview (Mapping Mutations on KEGG pathway)

1.Data Input

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.