brca_exchange_annotate_maf: Annotate BRCA1/2 variants

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

Annotate BRCA1/2 variants

Description

Adds functional BRCA1 and BRCA2 variant annotation, using BRCA Exchange API (see URL). Annotation comes from ENIGMA and ClinVar. Not that variant alleles in a MAF are in the column Tumor_Seq_Allele2 by default.

Usage

query_brca_exchange(gene, start, end, ref, alt, use_api = FALSE)

brca_annotate_maf(maf, use_api = FALSE)

Arguments

gene	Query gene.
start	Variant start position, in hg19.
end	Variant end position, in hg19.
ref	Reference allele.
alt	Alternate allele.
use_api	If TRUE uses BRCA exchange API, otherwise static table.
maf	Input MAF.

Value

Annotated MAF with columns brca_exchange_enigma, brca_exchange_clinvar variant annotation from ENIGMA and ClinVar, respectively, and brca_exchange_id indicating database variant ID.

Source

https://brcaexchange.org

Examples

query_brca_exchange('BRCA1', 41276045, 41276046, 'CT', '-')
  

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