gatk_haplotypecaller: gatk_haplotypecaller

In mskilab/skitools: Various mskilab R utilties

gatk_haplotypecaller

Description

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

intervals are given as GRanges

Usage

gatk_haplotypecaller(
  outdir,
  bams,
  intervals = NULL,
  dbsnp = Sys.getenv("GATK.DBSNP"),
  hg = Sys.getenv("GATK.FASTA"),
  genome = "hg19",
  outroot = "out",
  stand_call_conf = 30,
  stand_emit_conf = 2,
  min_mapq = 20,
  other.args = "",
  run = F,
  verbose = T,
  write_bam = F,
  oncotate = T
)

Arguments

outdir	out directory to output to
bams	bams to run variant calling on
intervals	GRanges intervals to run haplotype caller on
dbsnp	dbSNP path (=Sys.getenv('GATK.DBSNP'))
hg	genome fasta location (=Sys.getenv('GATK.FASTA'))
genome	name of genome build (='hg19')
outroot	prefix to give output files (='out')
stand_call_conf	confidence for calls (=30)
stand_emit_conf	confience for emission (=30)
min_mapq	minimum mapping quality (=20)
run	logical flag whether to run immediately or just return character vector of command (= FALSE)
verbose	logical flag (=TRUE)
write_bam	logical flag whether to write the bam (=FALSE)
oncotate	logical flag whether to oncotate output into MAF files (=TRUE)
other.arg	other arguments to give to haplotype caller (=”)

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.