run_gatk: Run GATK

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run GATK

Description

Runs the GATK suite of programs.

Usage

run_gatk(
  command = NULL,
  input = NULL,
  output = NULL,
  reference = NULL,
  normal.sample = NULL,
  intervals = NULL,
  known.sites = NULL,
  sample.map = NULL,
  erc = NULL,
  temp = NULL,
  batch = NULL,
  threads = NULL,
  database = NULL,
  bqsr = NULL,
  vqsr = NULL,
  tranches = NULL,
  resources = NULL,
  annotations = NULL,
  mode = NULL,
  tranches.file = NULL,
  sensitivity.filter = NULL,
  variant.index = TRUE,
  variant.type = NULL,
  select.method = NULL,
  filter.expression = NULL,
  filter.name = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  gatk = NULL
)

Arguments

command	GATK command to run, required
input	List of sorted bam files, required
output	List of output files or empty/non-existant directory
reference	Path to the fasta formatted reference
normal.sample	sample name of normal
intervals	Path to the intrvals list file, usually the exome coordiantes file
known.sites	List of paths to the files containing known polymorphic sites
sample.map	Path to tab seperated file mapping sample names to the gvcf file
erc	Mode for emitting reference confidence scores, can be "NONE", "BP_RESOLUTION" and "GVCF"
temp	Path to temporary directory
batch	Batch size fior number of readers open at once,GenomicsDBImport only
threads	Number of threads for opening VCFs in batches
database	Name of the database directory
bqsr	List of base quality recalibration files
vqsr	Varian recalibration file
tranches	List of levels of truth sensitivity at which to slice the data
resources	Pre defined list of sites for which to apply a prior probability of being correct
annotations	List ofnames of the annotations to be used for calculations
mode	Recalibration mode to employ, SNP or INDEL
tranches.file	The input tranches file describing where to cut the data, from VariantRecalibrator
sensitivity.filter	The truth sensitivity level at which to start filtering
variant.index	Create a VCF index when writing a coordinate-sorted VCF file, boolean, default set to TRUE
variant.type	Variant type to include in output, SNP or INDEL.
select.method	Method to select filtered vaiants, to select only variant that pass all filters use 'vc.isNotFiltered()'
filter.expression	String of filters and values
filter.name	Name to identify the filtered variants
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
gatk	Path to the GATK suit of programs, required

Value

List of GATK commands

Examples

## Not run: 
known.site.list <- c("Mills_and_1000G_gold_standard.indels.GRCh38.vcf.gz",
                      "1000G_phase1.snps.high_confidence.GRCh38.vcf.gz")

recalibration.files <- gsub(".bam","_recal_data.table",rg.bam.files)
command <-  "BaseRecalibrator"
fasta <- Path the genome fats
# BaseRecalibration
base.recalibration.cmds <- run_gatk(command = command,
                                    input = rg.bam.files,
                                    output = recalibration.files,
                                    reference = fasta,
                                    intervals = intervals.file,
                                    known.sites = known.site.list,
                                    execute = TRUE,
                                    gatk = gatk)

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.