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annotateMaf

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A set of functions to add variant annotation to a MAF file. Sources currently include OncoKB, BRCA Exchange and somatic hotspots from the Taylor Lab.

Installation

This package python modules urllib3 and ga4gh, the latter of which only works in python (< 3.0).
2019-02-14: Disabled due to this issue. Instead of querying the API, we now use a static table.

Load and install the library this way:

devtools::install_github('taylor-lab/annotateMaf')
library(annotateMaf)

Examples

Run the functions simply with your MAF (as a data.table, not the file path) as the input.

hotspot_annotate_maf requires a VEP-annotated MAF file.

# Note that the BRCA Exchange database is geared towards germline variants but by default the variant allele in a MAF is called Tumor_Seq_Allele2
annotated_maf = brca_exchange_annotate_maf(input_maf)

# Only retain oncogenic or likely oncogenic mutations after OncoKB annotation
maf %>% 
    oncokb_annotate_maf(input_maf) %>% 
    filter(oncogenic %like% 'Oncogenic)

Annotation sources:

  • OncoKB: Queries latest version of OncoKB, version number included but currently no support for querying older versions.
  • BRCA Exchange: Queries latest version of BRCA Exchange, also currently does not support versioning.
  • Somatic hotspots: List generated from PMIDs 26619011, 29247016, 28115009. Semi-manual curation was carried out to remove false-positive germline variants that were in the oldest publication.