realign_loosereads: realign_loosereads

In mskilab/loosends: Classifying loose ends in gGraphs

realign_loosereads

Description

Realign reads to selected reference

Usage

realign_loosereads(
  bam,
  ref = system.file("extdata", "hg19_looseends", "human_g1k_v37_decoy.fasta", package =
    "loosends"),
  bowtie = FALSE,
  bowtie.dir = system.file("extdata", "hg19_loosends", package = "loosends"),
  outdir = "./",
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

bam	(character) path to bam file
ref	(character) path to BWA indexed reference. If running bowtie then this should be basename of the indexed reference file
bowtie	(logical) use Bowtie2 aligner? default FALSE
bowtie.dir	(logical) directory containing bowtie files
outdir	(character) output directory to dump results
overwrite	(logical) overwrite existing analysis
verbose	(logical)

Value

path to output bam file with realigned reads

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.