Workflow: varscan somatic workflow

Fetched 2019-11-13 23:12:50 GMT
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Inputs

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

Steps

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

Outputs

ID Type Label Doc
indels File
loh_hc_indels File
germline_indels File
loh_snvs File
snvs File
somatic_indels File
germline_hc_indels File
germline_snvs File
somatic_snvs File
loh_hc_snvs File
loh_indels File
somatic_hc_indels File
germline_hc_snvs File
somatic_hc_snvs File
Permalink: https://w3id.org/cwl/view/git/8438316338e66823e1c9aca9f675b2bf33f2aa59/definitions/subworkflows/varscan.cwl