gatk_callvariants | R Documentation |
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.
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
)
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) |
Marcin Imielinski
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