annovarToMaf: Converts annovar annotations into MAF.

In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

Description

Converts variant annotations from Annovar into a basic MAF.

Usage

annovarToMaf(
  annovar,
  Center = NULL,
  refBuild = "hg19",
  tsbCol = NULL,
  table = "refGene",
  ens2hugo = TRUE,
  basename = NULL,
  sep = "\t",
  MAFobj = FALSE,
  sampleAnno = NULL
)

Arguments

annovar	input annovar annotation file. Can be vector of multiple files.
Center	Center field in MAF file will be filled with this value. Default NA.
refBuild	NCBI_Build field in MAF file will be filled with this value. Default hg19.
tsbCol	column name containing Tumor_Sample_Barcode or sample names in input file.
table	reference table used for gene-based annotations. Can be 'ensGene' or 'refGene'. Default 'refGene'
ens2hugo	If 'table' is 'ensGene', setting this argument to 'TRUE' converts all ensemble IDs to hugo symbols.
basename	If provided writes resulting MAF file to an output file.
sep	field seperator for input file. Default tab seperated.
MAFobj	If TRUE, returns results as an MAF object.
sampleAnno	annotations associated with each sample/Tumor_Sample_Barcode in input annovar file. If provided it will be included in MAF object. Could be a text file or a data.frame. Ideally annotation would contain clinical data, survival information and other necessary features associated with samples. Default NULL.

Details

Annovar is one of the most widely used Variant Annotation tools in Genomics. Annovar output is generally in a tabular format with various annotation columns. This function converts such annovar output files into MAF. This function requires that annovar was run with gene based annotation as a first operation, before including any filter or region based annotations. Please be aware that this function performs no transcript prioritization.

e.g, table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol (refGene),cytoBand,dbnsfp30a -operation (g),r,f -nastring NA

This function mainly uses gene based annotations for processing, rest of the annotation columns from input file will be attached to the end of the resulting MAF.

Value

MAF table.

References

Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38, e164 (2010).

Examples

var.annovar <- system.file("extdata", "variants.hg19_multianno.txt", package = "maftools")
var.annovar.maf <- annovarToMaf(annovar = var.annovar, Center = 'CSI-NUS', refBuild = 'hg19',
tsbCol = 'Tumor_Sample_Barcode', table = 'ensGene')

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.