reads.to.walks: reads.to.walks

In mskilab/skitools: Various mskilab R utilties

reads.to.walks

Description

Utility function to realign reads to walks.

Takes bam and collection of walks (GRanges list of signed intervals on hg19 or other BSgenome) pulls reads in regions of walks, then uses bwa mem to realign reads to walks, returns paths to new bams These bams are in "walk coordinates"

Assumes bwa mem installed an runnable from command line.

Usage

reads.to.walks(
  bam,
  walks,
  outdir = "./test",
  hg = skidb::read_hg(fft = T),
  mc.cores = 1,
  insert.size = 1000,
  verbose = T
)

Arguments

bam	path to bam file
walks	GRangesList of walks
outdir	outdir to compute into
hg	human genome sequence BSGenome or ffTrack
mc.cores	number of cores
insert.size	>= max insert size of library so that all relevant read pairs are extracted from the original bam

Value

paths to new bams These bams are in "walk coordinates"

mskilab/skitools documentation built on March 5, 2025, 11:52 p.m.