indexVcf {VariantAnnotation}R Documentation

Create Index files for VCF file

Description

Create Index file for VCF if it 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

Either character(), VcfFile, or VcfFileList

...

Additional arguments to indexTabix

Details

If a character vector is given, assumes they are the path(s) to the VCF file. If the index file for that VCF file does not exist, one is created. 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 1.28.13 Index]