Workflow: wgs alignment and germline variant detection

Fetched 2020-11-28 10:25:06 GMT
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Inputs

ID Type Title Doc
omni_vcf File
picard_metric_accumulation_level String
variant_reporting_intervals File
vep_cache_dir String (Optional)
mills File
bams File[]
hgvs_annotation Boolean (Optional)
gvcf_gq_bands String[]
known_indels File
emit_reference_confidence String
reference String
intervals e945b561aae8ddeff62c49553a95529f[]
synonyms_file File (Optional)
dbsnp_vcf File
qc_intervals File
readgroups String[]
coding_only Boolean (Optional)
custom_gnomad_vcf File (Optional)

Steps

ID Runs Label Doc
alignment_and_qc
wgs_alignment.cwl (Workflow)
wgs alignment with qc
detect_variants exome alignment and germline variant detection
extract_freemix
germline_wgs_workflow.cwl#extract_freemix/5c6e87fb-9fa2-4ade-8338-3252adf1ec17 (ExpressionTool)

Outputs

ID Type Label Doc
coding_vcf File
vep_summary File
gvcf File[]
final_vcf File
mark_duplicates_metrics File
wgs_metrics File
limited_vcf File
insert_size_metrics File
insert_size_histogram File
gc_bias_metrics_summary File
verify_bam_id_depth File
gc_bias_metrics_chart File
gc_bias_metrics File
cram File
verify_bam_id_metrics File
alignment_summary_metrics File
flagstats File
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/germline_wgs_workflow.cwl