gatk_haplotypecaller | R Documentation |
calls haplotype caller on a set of input bams and a given set of targets, outputting to target.dir
intervals are given as GRanges
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
)
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 (=”) |
character vector of command(s) (only if run = FALSE), otherwise just runs command with system call.
Marcin Imielinski
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.