View source: R/somaticStrelka2Manta.R
Somatic SNVs and SVs calling using Strelka2 and Manta
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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"
)
|
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'. |
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