View source: R/somaticStrelka2Manta.R
SVs calling of paired tumor-normal wgs using strelka2
SVs calling of paired tumor-normal wgs using strelka2
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | 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"
)
|
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 |
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