Workflow: Varscan Workflow

Fetched 2024-04-23 04:30:04 GMT
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Workflow as SVG
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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/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/varscan_germline.cwl