Import BAM file into GRanges

Description

Import aligned reads from a BAM file into a GRanges object.

Usage

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bam2GRanges(bamfile, bamindex = bamfile, chromosomes = NULL,
  pairedEndReads = FALSE, remove.duplicate.reads = FALSE, min.mapq = 10,
  max.fragment.width = 1000, blacklist = NULL, what = "mapq")

Arguments

bamfile

A sorted BAM file.

bamindex

BAM index file. Can be specified without the .bai ending. If the index file does not exist it will be created and a warning is issued.

chromosomes

If only a subset of the chromosomes should be imported, specify them here.

pairedEndReads

Set to TRUE if you have paired-end reads in your BAM files (not implemented for BED files).

remove.duplicate.reads

A logical indicating whether or not duplicate reads should be removed.

min.mapq

Minimum mapping quality when importing from BAM files. Set min.mapq=NULL to keep all reads.

max.fragment.width

Maximum allowed fragment length. This is to filter out erroneously wrong fragments due to mapping errors of paired end reads.

blacklist

A GRanges or a bed(.gz) file with blacklisted regions. Reads falling into those regions will be discarded.

what

A character vector of fields that are returned. Type scanBamWhat to see what is available.

Value

A GRanges object containing the reads.

Examples

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## Get an example BAM file with single-cell-sequencing reads
bamfile <- system.file("extdata", "BB150803_IV_074.bam", package="AneuFinderData")
## Read the file into a GRanges object
reads <- bam2GRanges(bamfile, chromosomes=c(1:19,'X','Y'), pairedEndReads=FALSE,
                    min.mapq=10, remove.duplicate.reads=TRUE)
print(reads)

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