compIdent_bamRcnt {GenVisR} | R Documentation

## Count nucleotide reads at SNP locations

### Description

Given the bam file path, count the number of reads at specified snp locations

### Usage

    compIdent_bamRcnt(bamfile, genome, target = NULL, debug = FALSE)

### Arguments

`bamfile` | Path to the bam file
`genome` | Object of class BSgenome corresponding to a genome of interest
`target` | Object of class data frame containing target locations in 1-base format and containing columns "chr", "start", "end", "var", "name"
`debug` | Boolean specifying if test datasets should be used for debugging.

### Value

object of class data frame containing readcount information

[Package GenVisR version 1.8.1 Index]