run_cuteSV: Run cuteSV

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

Run cuteSV

Description

cuteSV, a long-read-based structural variant detection program

Usage

run_cuteSV(
  input = NULL,
  reference = NULL,
  sample.names = NULL,
  bed = NULL,
  out.dir = NULL,
  platform = NULL,
  max_cluster_bias_INS = NULL,
  diff_ratio_merging_INS = NULL,
  max_cluster_bias_DEL = NULL,
  diff_ratio_merging_DEL = NULL,
  min_mapq = NULL,
  min_support = NULL,
  min_size = NULL,
  max_size = NULL,
  min_read_length = NULL,
  parallel = FALSE,
  cores = 4,
  execute = FALSE,
  cuteSV = NULL,
  version = FALSE
)

Arguments

input	List of sorted bam files, required
reference	Path to the fasta formatted reference
sample.names	List of the sample names
bed	Only detect SVs in regions in the BED file
out.dir	Name of the directory from the cuteSV output
platform	Names of the sequencing platform, choose either "ONT", "PacBio_CLR", "PacBio_CCS" or "FORCE"
max_cluster_bias_INS	Maximum distance to cluster reads together for insertion.
diff_ratio_merging_INS	Do not merge breakpoints with basepair identity more than [0.3] for insertion.
max_cluster_bias_DEL	Maximum distance to cluster read together for deletion.
diff_ratio_merging_DEL	Do not merge breakpoints with basepair identity more than [0.5] for deletion.
min_mapq	Minimum mapping quality value of alignment to be taken into account.
min_support	Minimum number of reads that support a SV to be reported.
min_size	Minimum size of SV to be reported.
max_size	Maximum size of SV to be reported. All SVs are reported when using -1
min_read_length	Minimum read alignment length
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
cuteSV	Path to the cuteSV program, required
version	Returns the version number

Value

A list with the Minimap2 commands

Examples

## Not run: 
cuteSV.path <- "path/to/cuteSV"

run_cuteSV(cuteSV = cuteSV.path,
           version = TRUE)

out.dir <- "VCF"
sample.names <- c("sample_1","sample_2","sample_3")
sorted.bam.files <- c("sample_1.bam","sample_2.bam","sample_3.bam")
genome = "/datastore/Gneomes/Reference/genome.fa"

run_cuteSV(input = sorted.bam.files,
           reference = genome,
           sample.names = sample.names,
           out.dir =out.dir,
           platform = "ONT",
           cuteSV = cuteSV.path)

## End(Not run)

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