Workflow: exome alignment with qc

Fetched 2019-05-20 23:28:02 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 File
bams File[]
target_intervals File
known_indels File
per_target_intervals File
reference String
bait_intervals File
qc_minimum_base_quality Integer (Optional)
per_base_bait_intervals File
dbsnp_vcf File
readgroups String[]
per_target_bait_intervals File

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 (Optional)
mark_duplicates_metrics File
per_base_hs_metrics File (Optional)
insert_size_metrics File
insert_size_histogram File
verify_bam_id_depth File
hs_metrics File
cram File
alignment_summary_metrics File
verify_bam_id_metrics File
per_target_hs_metrics File (Optional)
flagstats File
per_base_coverage_metrics File (Optional)
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/exome_alignment.cwl