README.md

In kpjonsson/annotate-maf: Functional Annotation of Variants in a MAF File

annotateMaf

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.

kpjonsson/annotate-maf documentation built on Nov. 25, 2024, 8:10 a.m.