Variant Annotation Resources

Tool

TransVar

Zhou W., Chen T., Chong Z., Rohrdanz M.A., Melott J.M., Wakefield C., Zeng J., Weinstein J.M., Meric-Bernstam F., Mills G.B., et al. TransVar: A multilevel variant annotator for precision genomics. Nat. Methods. 2015;12:1002. doi: 10.1038/nmeth.3622. GitHub Link

• A multi-way annotator for genetic elements and genetic variations
• Operates on
  • genomic coordinates
    • chr3:g.178936091G>A
  • and transcript-dependent cDNA as well as protein coordinates
    • PIK3CA:p.E545K or PIK3CA:c.1633G>A
    • or NM_006218.2:p.E545K, or NP_006266.2:p.G240Afs*50
• and was designed to resolve ambiguous mutation annotations arising from differential transcript usage.
• Supports
  • HGVS nomenclature
  • both left-alignment and right-alignment convention in reporting indels
  • annotation of a region based on a transcript dependent characterization
  • single nucleotide variation (SNV), insertions and deletions (indels) and block substitutions
  • mutations at both coding region and intronic/UTR regions
  • transcript annotation from commonly-used databases such as Ensembl, NCBI RefSeq and GENCODE etc
  • UniProt protein id as transcript id
  • GRCh36, 37, 38
  • forward annotation

OpenCRAVAT

Pagel KA et al. Integrated Informatics Analysis of Cancer-Related Variants. JCO Clinical Cancer Informatics 2020 4, 310-317. doi: 10.1200/CCI.19.00132 GitHub Link

• A python package that performs genomic variant interpretation including variant impact, annotation, and scoring
• Has a modular architecture with a wide variety of analysis modules that can be selected and installed/run based on the needs of a given study
• It takes a file of genomic variants as input.
  • The most common input format is a VCF file but other formats are supported including dbSNP identifiers, 23&Me and Ancestry.com file formats.
• The analysis performed by OpenCRAVAT depends upon user-selected annotation and visualization options, available for download from the free OpenCRAVAT Store.
• In addition to the interactive user interface, OpenCRAVAT provides several output formats including text reports, Excel spreadsheets, and a SQLite database of results used by cravat_view.
• When the pipeline program is run, it will execute a series of modules required for variant analysis.
  • First, the appropriate converter will be run to parse the input variant file.
  • Next, a mapper module will determine the transcripts and associated genes affected by each variant including protein impact.
  • Then OpenCRAVAT runs all of the requested/installed annotation modules and after all annotation is complete, an aggregator program collects and collates the results into a SQLite database.
  • Finally, reporter modules are run to produce the requested format of results.

Annovar

Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data. Nucleic Acids Research, 38:e164, 2010

• An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes
  • including human genome hg18, hg19, hg38
  • as well as mouse, worm, fly, yeast and many others
• Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform:
  • Gene-based annotation
  • Region-based annotation
  • Filter-based annotation
  • Other functionalities