Workflow: Filter single sample sv vcf from paired read callers(Manta/Smoove)

Fetched 2022-01-20 08:43:57 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
duplication_depth Double (Optional)
reference String
sv_vcf File
deletion_depth Double (Optional)
output_vcf_name String (Optional)
vcf_source
sv_paired_count Integer (Optional)
snps_vcf File (Optional)
abundance_percentage Double (Optional)
sv_split_count Integer (Optional)
bam File

Steps

ID Runs Label Doc
depth_filter
../tools/filter_sv_vcf_depth.cwl (CommandLineTool)
filtered_vcf_bgzip
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
duphold_annotate
../tools/duphold.cwl (CommandLineTool)
read_support_filter
../tools/filter_sv_vcf_read_support.cwl (CommandLineTool)
filtered_vcf_index
../tools/index_vcf.cwl (CommandLineTool)
vcf index

Outputs

ID Type Label Doc
filtered_vcf File
Permalink: https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/sv_paired_read_caller_filter.cwl