Workflow: Unaligned BAM to BQSR

Fetched 2023-01-04 20:13:43 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
bams File[]
reference String
final_name String
readgroups String[]
bqsr_intervals String[] (Optional)
bqsr_known_sites File[]

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

Steps

ID Runs Label Doc
bqsr
../tools/bqsr.cwl (CommandLineTool)
create BQSR table
align
align.cwl (Workflow)
Unaligned to aligned BAM
merge
../tools/merge_bams_samtools.cwl (CommandLineTool)
Samtools: merge
index_bam
../tools/index_bam.cwl (CommandLineTool)
samtools index
name_sort
../tools/name_sort.cwl (CommandLineTool)
sort BAM by name
apply_bqsr
../tools/apply_bqsr.cwl (CommandLineTool)
apply BQSR
mark_duplicates_and_sort
../tools/mark_duplicates_and_sort.cwl (CommandLineTool)
Mark duplicates and Sort

Outputs

ID Type Label Doc
final_bam File
mark_duplicates_metrics_file File
Permalink: https://w3id.org/cwl/view/git/480c438a6a7e78c624712aec01bc4214d2bc179c/definitions/subworkflows/bam_to_bqsr.cwl