Workflow: exome alignment and germline variant detection

Fetched 2023-01-12 08:37:44 GMT
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Inputs

ID Type Title Doc
bams File[]
mills File
omni_vcf File
dbsnp_vcf File
intervals b45a6f7de178f24f0df7fe4962337391[]
reference String
readgroups String[]
known_indels File
gvcf_gq_bands String[]
synonyms_file File (Optional)
vep_cache_dir String (Optional)
bait_intervals File
bqsr_intervals String[] (Optional)
hgvs_annotation Boolean (Optional)
target_intervals File
custom_gnomad_vcf File (Optional)
summary_intervals https://w3id.org/cwl/view/git/de81bd20ce8829ef64146115902a10e4fe7bad0b/definitions/types/labelled_file.yml#labelled_file[]
custom_clinvar_vcf File (Optional)
per_base_intervals https://w3id.org/cwl/view/git/de81bd20ce8829ef64146115902a10e4fe7bad0b/definitions/types/labelled_file.yml#labelled_file[]
annotate_coding_only Boolean (Optional)
per_target_intervals https://w3id.org/cwl/view/git/de81bd20ce8829ef64146115902a10e4fe7bad0b/definitions/types/labelled_file.yml#labelled_file[]
qc_minimum_base_quality Integer (Optional)
emit_reference_confidence String
qc_minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
detect_variants exome alignment and germline variant detection
extract_freemix
germline_exome.cwl#extract_freemix/4d9ed46c-253d-4529-a5ab-f1e0ec0a5ce3 (ExpressionTool)
alignment_and_qc
exome_alignment.cwl (Workflow)
exome alignment with qc

Outputs

ID Type Label Doc
cram File
gvcf File[]
final_vcf File
flagstats File
coding_vcf File
hs_metrics File
limited_vcf File
vep_summary File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/de81bd20ce8829ef64146115902a10e4fe7bad0b/definitions/pipelines/germline_exome.cwl