seqminer (version 9.7)

tabix.createIndex: Create tabix index file, similar to running tabix in command line.

Description

Create tabix index file, similar to running tabix in command line.

Usage

tabix.createIndex(
  bgzipFile,
  sequenceColumn = 1,
  startColumn = 4,
  endColumn = 5,
  metaChar = "#",
  skipLines = 0
)

Arguments

bgzipFile

character, an tabix indexed file

sequenceColumn

integer, sequence name column

startColumn

integer, start column

endColumn

integer, end column

metaChar

character, symbol for comment/meta lines

skipLines

integer, first this number of lines will be skipped

See Also

http://zhanxw.com/seqminer/ for online manual and examples

Examples

fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
tabix.createIndex(fileName, 1, 2, 0, '#', 0)