strelka2: strelka2

In msubirana/DNAseqPipeline: What the Package Does (One Line, Title Case)

Description

SVs calling of paired tumor-normal wgs using strelka2

SVs calling of paired tumor-normal wgs using strelka2

Usage

strelka2(
  tumor_bam,
  ctrl_bam,
  ref,
  out_dir_strelka2,
  cores,
  conf_strelka2 = "configureStrelkaSomaticWorkflow.py",
  indel_candidates,
  call_regions = "/gpfs42/projects/lab_lpasquali/shared_data/ref/callRegions.bed.gz"
)

strelka2(
  tumor_bam,
  ctrl_bam,
  ref,
  out_dir_strelka2,
  cores,
  conf_strelka2 = "configureStrelkaSomaticWorkflow.py",
  indel_candidates,
  call_regions = "/gpfs42/projects/lab_lpasquali/shared_data/ref/callRegions.bed.gz"
)

Arguments

ref	Reference fasta genome. By default '/gpfs42/projects/lab_lpasquali/shared_data/marc/ref/hg38/hg38.fa'
out_dir_strelka2	Path where the output of the Strelka2 analysis will be saved.
cores	Number of cores to use.
conf_strelka2	Strelka2 'configureStrelkaGermlineWorkflow.py' path. By default 'configureStrelkaGermlineWorkflow.py'.
indel_candidates	'candidateSmallIndels.vcf.gz' file from Manta calling. It is a recommended best practice to provide indel candidates from the Manta SV and indel caller.
call_regions	Manta calls the entire genome by default, however variant calling may be restricted to an arbitrary subset of the genome by providing a region file in BED format with the –callRegions configuration option. The BED file must be bgzip-compressed and tabix-indexed, and only one such BED file may be specified. When specified, all VCF output is restricted to the provided call regions only, however statistics derived from the input data

msubirana/DNAseqPipeline documentation built on Dec. 21, 2021, 10:12 p.m.