Workflow: varscan somatic workflow

Fetched 2024-02-28 22:45:57 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
p_value Float (Optional)
roi_bed File (Optional)
reference File
tumor_bam File
normal_bam File
min_coverage Integer (Optional)
min_var_freq Float (Optional)
strand_filter Integer (Optional)
max_normal_freq Float (Optional)

Steps

ID Runs Label Doc
somatic
../tools/varscan_somatic.cwl (CommandLineTool)
varscan v2.4.2 somatic
process_somatic_snvs
../tools/varscan_process_somatic.cwl (CommandLineTool)
varscan v2.4.2 processSomatic
process_somatic_indels
../tools/varscan_process_somatic.cwl (CommandLineTool)
varscan v2.4.2 processSomatic

Outputs

ID Type Label Doc
snvs File
indels File
loh_snvs File
loh_indels File
loh_hc_snvs File
somatic_snvs File
germline_snvs File
loh_hc_indels File
somatic_indels File
germline_indels File
somatic_hc_snvs File
germline_hc_snvs File
somatic_hc_indels File
germline_hc_indels File
Permalink: https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/subworkflows/varscan.cwl