indexVcf {VariantAnnotation} | R Documentation |
Create Index file for VCF if it does not exist
## S4 method for signature 'character' indexVcf(x, ...) ## S4 method for signature 'VcfFile' indexVcf(x, ...) ## S4 method for signature 'VcfFileList' indexVcf(x, ...)
x |
Either character(), |
... |
Additional arguments to |
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.
VcfFile or VcfFileList
Lori Shepherd
fl <- system.file("extdata", "chr7-sub.vcf.gz", package="VariantAnnotation", mustWork=TRUE) vcf1 <- indexVcf(fl) vcf1