strelka2: strelka2

Description Usage Arguments

View source: R/somaticStrelka2Manta.R

Description

SVs calling of paired tumor-normal wgs using strelka2

SVs calling of paired tumor-normal wgs using strelka2

Usage

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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.