Workflow: Varscan Workflow

Fetched 2023-01-04 10:33:55 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
bam File
p_value Float (Optional)
min_reads Integer (Optional)
reference File
sample_name String
min_coverage Integer (Optional)
min_var_freq Float (Optional)
interval_list File
strand_filter Integer (Optional)
max_normal_freq Float (Optional)

Steps

ID Runs Label Doc
filter
fp_filter.cwl (Workflow)
fp_filter workflow
varscan
../tools/varscan_germline.cwl (CommandLineTool)
varscan v2.4.2 germline
bgzip_and_index
bgzip_and_index.cwl (Workflow)
bgzip and index VCF
intervals_to_bed
../tools/intervals_to_bed.cwl (CommandLineTool)

Outputs

ID Type Label Doc
filtered_vcf File
unfiltered_vcf File
Permalink: https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/subworkflows/varscan_germline.cwl