Workflow: phase VCF

Fetched 2023-01-09 22:27:10 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs tumor_sample_name tumor_sample_name rename_germline_vcf rename_germline_vcf tumor_sample_name->rename_germline_vcf new_sample_name select_somatic_tumor_sample SelectVariants (GATK 4.1.8.1) tumor_sample_name->select_somatic_tumor_sample samples_to_include reference reference phase_vcf Read-backed phasing reference->phase_vcf reference reference->select_somatic_tumor_sample reference combine_variants Combine germline and somatic vcf for pVACseq phasing reference->combine_variants reference bam bam bam->phase_vcf bam germline_vcf germline_vcf germline_vcf->rename_germline_vcf input_vcf somatic_vcf somatic_vcf somatic_vcf->select_somatic_tumor_sample vcf normal_sample_name normal_sample_name normal_sample_name->rename_germline_vcf sample_to_replace reference_dict reference_dict sort Sort VCF reference_dict->sort reference_dict phased_vcf phased_vcf bgzip_and_index_phased_vcf bgzip and index VCF phase_vcf->bgzip_and_index_phased_vcf vcf index_renamed_germline vcf index index_renamed_germline->combine_variants germline_vcf bgzip_and_index bgzip and index VCF sort->bgzip_and_index vcf rename_germline_vcf->index_renamed_germline vcf index_filtered_somatic vcf index select_somatic_tumor_sample->index_filtered_somatic vcf bgzip_and_index_phased_vcf->phased_vcf index_filtered_somatic->combine_variants somatic_vcf combine_variants->sort vcf bgzip_and_index->phase_vcf vcf default1 "somatic_tumor_only" default1->select_somatic_tumor_sample output_vcf_basename
Workflow as SVG
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  • Inputs/Outputs

Inputs

ID Type Title Doc
bam File
reference File
somatic_vcf File
germline_vcf File
reference_dict File
tumor_sample_name String
normal_sample_name String

Steps

ID Runs Label Doc
sort
../tools/sort_vcf.cwl (CommandLineTool)
Sort VCF
phase_vcf
../tools/read_backed_phasing.cwl (CommandLineTool)
Read-backed phasing
bgzip_and_index
bgzip_and_index.cwl (Workflow)
bgzip and index VCF
combine_variants
../tools/pvacseq_combine_variants.cwl (CommandLineTool)
Combine germline and somatic vcf for pVACseq phasing
rename_germline_vcf
../tools/replace_vcf_sample_name.cwl (CommandLineTool)
index_filtered_somatic
../tools/index_vcf.cwl (CommandLineTool)
vcf index
index_renamed_germline
../tools/index_vcf.cwl (CommandLineTool)
vcf index
bgzip_and_index_phased_vcf
bgzip_and_index.cwl (Workflow)
bgzip and index VCF
select_somatic_tumor_sample
../tools/select_variants.cwl (CommandLineTool)
SelectVariants (GATK 4.1.8.1)

Outputs

ID Type Label Doc
phased_vcf File
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/subworkflows/phase_vcf.cwl