Workflow: Unaligned BAM to BQSR and VCF

Fetched 2021-09-21 23:43:29 GMT
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Workflow as SVG
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Inputs

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

Steps

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

Outputs

ID Type Label Doc
final_bam File
mark_duplicates_metrics_file File
Permalink: https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bam_to_bqsr.cwl