get_snv_read_count: Get Nucleotide Read Counts

In tinyheero/tinyutils: Utility Functions to Assist With Data Analysis

Description

Wrapper function over Rsamtools::pileup to retrieve nucleotide read count values over a set of positions. This function serves more as a way to document how to use the pileup function.

Usage

get_snv_read_count(bamfile, scan.bam.param, pileup.param)

Arguments

bamfile	Path to the input bam file.
pileup.param	Rsamtools::PileupParam object which specifies specific pileup parameters for filtering.
scan.bam.params	Rsamtools::ScanBamParam object which specifies positions to lookup and additional read filtering. See the ScanBamParam documentation for specific details.

Value

data.frame containing the nucleotide and read count information for each position specified.

Examples

library("GenomicRanges")
library("Rsamtools")

bamfile <- system.file("extdata", "ex1.bam", package = "Rsamtools")

# Setup Lookup Positions 
positions.df <- data.frame(chr = c("seq1", "seq1", "seq1"),
                           start = c(50, 891, 1000),
                           stop = c(50, 891, 1000))
positions.gr <- makeGRangesFromDataFrame(positions.df)
scan.bam.param <- ScanBamParam(which = positions.gr)

# Setup Read Filters
pileup.param <- PileupParam(max_depth = 1000, min_mapq = 13, 
                            min_base_quality = 20, 
                            distinguish_strands = FALSE, 
                            min_nucleotide_depth = 0)

get_snv_read_count(bamfile, scan.bam.param)

tinyheero/tinyutils documentation built on May 31, 2019, 3:36 p.m.