somaticStrelka2Manta: somaticStrelka2Manta

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

Description

Somatic SNVs and SVs calling using Strelka2 and Manta

Usage

somaticStrelka2Manta(
  tumor_bam,
  ctrl_bam,
 
    ref = "/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa",
  out_dir_manta,
  out_dir_strelka2,
  cores,
  conf_manta = "configManta.py",
 
    call_regions = "/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/ref/callRegions.bed.gz",
  conf_strelka2 = "configureStrelkaSomaticWorkflow.py"
)

Arguments

tumor_bam	Tumor BAM file to use in the analysis
ctrl_bam	Tumor BAM file to use in the analysis
ref	Reference fasta genome. By default '/gpfs42/projects/lab_lpasquali/shared_data/marc/ref/hg38/hg38.fa'
out_dir_manta	Path where the output of the Manta analysis will be saved.
out_dir_strelka2	Path where the output of the Strelka2 analysis will be saved.
cores	Number of cores to use.
conf_manta	Manta 'configManta.py' path. By default 'configManta.py'
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
conf_strelka2	Strelka2 'configureStrelkaSomaticWorkflow.py' path. By default 'configureStrelkaSomaticWorkflow.py'.

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