indexVcf {VariantAnnotation} | R Documentation

## Create index files for VCF files

### Description

`indexVcf()` creates an index file for compressed VCF files, if the index file does not exist.

### Usage

    ## S4 method for signature 'character'
    indexVcf(x, ...)
    ## S4 method for signature 'VcfFile'
    indexVcf(x, ...)
    ## S4 method for signature 'VcfFileList'
    indexVcf(x, ...)

### Arguments

`x` | `character()`, `VcfFile`, or `VcfFileList` pointing to bgzf-compressed VCF files.
`...` | Additional arguments to `indexTabix`

### Details

If `x` is a character vector, assumes they are the path(s) to bgzf-compressed VCF file(s). If an index does not exist, one is created. VCF files can be compreseed using `bgzip`. A `VcfFile` or `VcfFileList` is returned.

If a `VcfFile` or `VcfFileList` is given, the index file is checked, if it does not exist it will crete one. If the index file was NA or missing, the path of the associated VCF file is used as the index file path. An updated `VcfFile` or `VcfFileList` is returned.

### Value

VcfFile or VcfFileList

### Author(s)

Lori Shepherd

### See Also

`VcfFile`

### Examples

    fl <- system.file(
        "extdata", "chr7-sub.vcf.gz", package="VariantAnnotation",
        mustWork=TRUE
    )
    vcf1 <- indexVcf(fl)
    vcf1

[Package VariantAnnotation version 1.33.4 Index]