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

readSingleChromosomeBCFToMatrixByRange {seqminer} | R Documentation

## 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")

[Package seqminer version 8.0 Index]