run_snpsift: Run SnpSift

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

Run SnpSift

Description

Runs the SnpSift program.

Usage

run_snpsift(
  command = NULL,
  input = NULL,
  output = NULL,
  filter = NULL,
  inverse = FALSE,
  dbsnp = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  snpsift = NULL
)

Arguments

command	SnpSift command to run, currently only fiter, annotate and vartype
input	Input file, vcf format
output	Name of output file, vcf format
filter	Filter expression
inverse	Show lines that do not match filter expression
dbsnp	Path to the dbsnp file
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
snpsift	Path to the SnpSift program, required

Value

List of SnpSift commands

Examples

## Not run: 
snpsift.path <- "/software/snpEff-v5.0e/SnpSift.jar"

run_snpsift(command = "filter",
            input = "file.vcf",
            output = "filtered.file.vcf",
            filter = "'( QUAL >= 30 )'",
            execute = FALSE,
            snpsift = snpsift.path)

run_snpsift(command = "annotate",
            input = "file.vcf",
            output = "annotated.file.vcf",
            dbsnp = "/datastore/GATK_resource_bundle/GRCh38/dbsnp_146.GRCh38.vcf.gz",
            execute = FALSE,
            snpsift = snpsift.path)

run_snpsift(command = "vartype",
            input = "file.vcf",
            output = "annotated.file.vcf",
            execute = FALSE,
            snpsift = snpsift.path)


## End(Not run)

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