pindel: pindel

In mskilab/skitools: Various mskilab R utilties

pindel

Description

calls pindel on a set of input bams and a given set of targets, outputting to target.dir

intervals are given as GRanges

Usage

pindel(
  outdir,
  bams,
  intervals = NULL,
  isizes = NULL,
  hg = Sys.getenv("GATK.FASTA"),
  genome = "hg19",
  outroot = "out",
  run = F,
  verbose = T,
  write_bam = F,
  oncotate = F,
  threads = 1,
  window.size = 10,
  other.args = ""
)

Arguments

outdir	out directory to output to
bams	vector of input bams
intervals	GRanges of to run on (=NULL)
isizes	integer insert.size to use
hg	genome fasta location (=Sys.getenv('GATK.HG19'))
genome	genome build (='hg19')
outroot	prefix to give output files (='out')
run	logical flag whether to run immediately or just return character vector of command (= FALSE)
verbose	logical flag
write_bam	logical flag whether to write the bam (=FALSE)
oncotate	logical flag whether to oncotate output into MAF files (=TRUE)
threads	number of threads to use
window.size	integer window size to use (=10)
other.args	other args to add (=”)

Value

character vector of command(s) (only if run = FALSE), otherwise just runs command with system call.

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.