countBamInGRanges.exomeDepth: Compute read count data from BAM files.

In drramki-chop/edm: Scalable workflow to identify copy Number variants from exome sequencing data

Description

Parses a BAM file and count reads that are located within a target region defined by a GenomicRanges object.

Usage

countBamInGRanges.exomeDepth(bam.file, index = bam.file, granges,
min.mapq = 1, read.width = 1)

Arguments

bam.file	BAM file to be parsed
index	Index of the BAM file, without the '.bai' suffix.
granges	Genomic ranges object defining the bins
min.mapq	Minimum read mapping quality (Phred scaled).
read.width	For single end reads, an estimate of the frament size. For paired reads, the fragment size can be directly computed from the paired alignment and this value is ignored.

Details

Largely derived from its equivalent function in the exomeCopy package.

Value

A GRanges object with count data.

drramki-chop/edm documentation built on June 6, 2020, 8:48 a.m.