readSampleNamesFromVcfHeader {podkat} | R Documentation

## Read Sample Names from VCF File Header

### Description

Reads the header of a VCF file and returns sample names as character vector

### Usage

    readSampleNamesFromVcfHeader(file, ...)

### Arguments

`file` | a `TabixFile` object or a character string with a file name of the VCF file to read from; if `file` is a file name, the method internally creates a `TabixFile` object for this file name.
`...` | all additional arguments are passed on internally to `scanBcfHeader` function from the `Rsamtools` package.

### Details

This function is a simple wrapper around the `scanBcfHeader` function from the `Rsamtools` package that scans the header of a VCF file and returns the sample names as a character vector.

### Value

a character vector with sample names

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

http://www.bioinf.jku.at/software/podkat

http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42

Li, H., Handsaker, B., Wysoker, A., Fenell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.

### See Also

`scanBcfHeader`

### Examples

    vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")
    readSampleNamesFromVcfHeader(vcfFile)

[Package podkat version 1.22.0 Index]