Workflow: Detect Variants workflow

Fetched 2021-01-14 15:48:44 GMT
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Inputs

ID Type Title Doc
reference File
pindel_insert_size Integer
cosmic_vcf File (Optional)
dbsnp_vcf File (Optional)
strelka_exome_mode Boolean
normal_bam File
interval_list File
tumor_bam File

Steps

ID Runs Label Doc
filter
fp_filter.cwl (CommandLineTool)
False Positive filter
varscan Varscan Workflow
index
index.cwl (CommandLineTool)
vcf index
bgzip
bgzip.cwl (CommandLineTool)
bgzip VCF
strelka strelka workflow
mutect mutect parallel workflow
combine
combine_variants.cwl (CommandLineTool)
CombineVariants (GATK 3.6)
pindel pindel parallel workflow

Outputs

ID Type Label Doc
final_vcf File
Permalink: https://w3id.org/cwl/view/git/5a67e91727c8eb44afff27f9e4774eafef579c58/detect_variants/detect_variants.cwl