readSingleChromosomeBCFToMatrixByRange: Read a range from BCF file and return a genotype matrix

In seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Read a range from BCF file and return a genotype matrix

Description

Read a range from BCF file and return a genotype matrix

Usage

readSingleChromosomeBCFToMatrixByRange(fileName, range, indexFileName = NULL)

Arguments

fileName	character, represents an input BCF file (Bgzipped, with Tabix index)
range	character, a text indicating which range in the BCF file to extract. e.g. 1:100-200, 1-based index
indexFileName	character, index file, by default, it s 'fileName'.scIdx

Value

genotype matrix

See Also

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

Examples

fileName = system.file("vcf/all.anno.filtered.extract.headerFixed.bcf.gz", package = "seqminer")
cfh <- readSingleChromosomeBCFToMatrixByRange(fileName, "1:196621007-196716634")

seqminer documentation built on Oct. 7, 2024, 1:15 a.m.