seqVCF_Header {SeqArray} | R Documentation

## Parse the Header of a VCF/BCF File

### Description

Parses the meta-information lines of a VCF or BCF file.

### Usage

    seqVCF_Header(vcf.fn, getnum=FALSE)

### Arguments

`vcf.fn` | the file name of VCF or BCF format; or a `connection` object for VCF format
`getnum` | if `TRUE`, return the total number of variants

### Details

The ID description contains four columns: `ID` – variable name; `Number` – the number of elements, see the webpage of the 1000 Genomes Project; `Type` – data type; `Description` – a variable description.

### Value

Return a list (with a class name "SeqVCFHeaderClass", S3 object):

`fileformat` | the file format
`info` | the ID description in the INFO field
`filter` | the ID description in the FILTER field
`format` | the ID description in the FORMAT field
`alt` | the ID description in the ALT field
`contig` | the description in the contig field
`assembly` | the link of assembly
`reference` | genome reference, or `NULL` if unknown
`header` | the other header lines
`ploidy` | ploidy, two for humans
`num.sample` | the number of samples
`num.variant` | the number of variants, applicable only if `getnum=TRUE`
`sample.id` | a vector of sample IDs in the VCF/BCF file

### Author(s)

Xiuwen Zheng

### References

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al. (2011). The variant call format and VCFtools. Bioinformatics 27, 2156-2158.

### See Also

`seqVCF_SampID`, `seqVCF2GDS`

### Examples

    # the VCF file
    (vcf.fn <- seqExampleFileName("vcf"))
    # or vcf.fn <- "C:/YourFolder/Your_VCF_File.vcf"

    # get sample id
    seqVCF_Header(vcf.fn, getnum=TRUE)

    # use a connection object
    f <- file(vcf.fn, "r")
    seqVCF_Header(f, getnum=TRUE)
    close(f)

[Package SeqArray version 1.26.2 Index]