gatk_callvariants: gatk_callvariants

gatk_callvariantsR Documentation

gatk_callvariants

Description

Outputs variant calling pipeline on a set of whole genome (or whole exome) bams to shell script and prints instructions on how to execute from command line.

Usage

gatk_callvariants(
  bams,
  outdir = "./",
  run = gsub("[^\\w+]", "_", as.character(Sys.time()), perl = T),
  queue = "hour",
  memlimit = 2,
  sep = "/",
  skipclean = T,
  chunk = 250000,
  runtype = "wg",
  dry = FALSE,
  dcov = 200,
  bsub = FALSE,
  vqsr.memlimit = memlimit
)

Arguments

bams

bams to run variant calling on

outdir

out directory to output to

run

name to give run (=timestamp)

queue

LSF queue to run on (='week')

memlimit

memory limit in GB

skipclean

logical flag whether to skipclean (=TRUE)

chunk

integer chunk of variants to run each section on (=250e3)

runtype

character run type (='wg')

dry

logical flag whether to do dry run (=FALSE)

dcov

dcov parameter to GATK (=200)

bsub

whether to run on LSF vs local (=FALSE)

Author(s)

Marcin Imielinski


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