annovarToMaf {maftools} | R Documentation

## Converts annovar annotations into MAF.

### 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')

[Package maftools version 2.0.16 Index]