Workflow: Exome QC workflow

Fetched 2019-03-18 18:23:17 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
reference File
omni_vcf File
bait_intervals File
collect_hs_metrics_per_target_coverage Boolean (Optional)
target_intervals File
bam File

Steps

ID Runs Label Doc
collect_alignment_summary_metrics
collect_alignment_summary_metrics.cwl (CommandLineTool)
collect alignment summary metrics
select_variants
../detect_variants/select_variants.cwl (CommandLineTool)
SelectVariants (GATK 3.6)
collect_insert_size_metrics
collect_insert_size_metrics.cwl (CommandLineTool)
collect insert size metrics
collect_hs_metrics
collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics
samtools_flagstat
samtools_flagstat.cwl (CommandLineTool)
samtools flagstat
verify_bam_id
verify_bam_id.cwl (CommandLineTool)
verify BAM ID

Outputs

ID Type Label Doc
per_target_coverage_metrics File (Optional)
hs_metrics File
verify_bam_id_metrics File
insert_size_metrics File
alignment_summary_metrics File
verify_bam_id_depth File
flagstats File
Permalink: https://w3id.org/cwl/view/git/8c5ae3dbabfe73e0a577b91b25ef5b0b32f388cb/qc/workflow_exome.cwl