Workflow: exome alignment with qc

Fetched 2021-07-28 09:26:58 GMT
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Inputs

ID Type Title Doc
omni_vcf File
picard_metric_accumulation_level String
bqsr_intervals String[] (Optional)
qc_minimum_mapping_quality Integer (Optional)
mills File
per_base_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
bams File[]
target_intervals File
known_indels File
reference String
per_target_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
bait_intervals File
qc_minimum_base_quality Integer (Optional)
dbsnp_vcf File
readgroups String[]
summary_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
final_name String (Optional)

Steps

ID Runs Label Doc
qc Exome QC workflow
alignment Unaligned BAM to BQSR and VCF

Outputs

ID Type Label Doc
per_target_coverage_metrics File[]
mark_duplicates_metrics File
insert_size_metrics File
per_base_hs_metrics File[]
insert_size_histogram File
verify_bam_id_depth File
summary_hs_metrics File[]
bam File
hs_metrics File
alignment_summary_metrics File
verify_bam_id_metrics File
per_target_hs_metrics File[]
flagstats File
per_base_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/pipelines/exome_alignment.cwl