annovarToMaf: Converts annovar annotations into MAF.
In maftools: Summarize, Analyze and Visualize MAF Files

Description Usage Arguments Details Value References Examples

Converts variant annotations from Annovar into a basic MAF.

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

`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.

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.

MAF table.

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

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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')

-Reading annovar files
-Processing Exonic variants
--Adding Variant_Classification
--Parsing aa-change
-Processing Non-exonic variants
--Adding Variant_Classification
-Adding Variant_Type
-Converting Ensemble Gene IDs into HGNC gene symbols
--Done. Original ensemble gene IDs are preserved under field name ens_id
Finished in 0.427s elapsed (0.335s cpu)