getProperAlignmentPairs: Extract properly paired reads from a bam file

In cancer-genomics/trellis: Somatic structural variant analysis

Extract properly paired reads from a bam file

Description

Function used by rearrangement analysis to extract the sequence of properly paired reads from a bam file.

Usage

getProperAlignmentPairs(
  bam.file,
  param = properAlignmentParams(mapqFilter = 0),
  build
)

Arguments

bam.file	a BamViews object
param	a ScanBamParam object.
build	the reference genome buld that reads were aligned to. Currently supported builds include "hg19" and "hg18".

Value

a GAlignmentPairs object

See Also

See properAlignmentParams for creating a ScanBamParam object with the appropriate flags for extracting proper read pairs.

Examples

library(svbams)
path <- system.file("extdata", package="svbams")
bam.file <- file.path(path, "cgov10t.bam")
irp <- getProperAlignmentPairs(bam.file, build="hg19")

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.