Workflow: Unaligned BAM to BQSR and VCF

Fetched 2021-06-17 09:03:38 GMT
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Workflow as SVG
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Inputs

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

Steps

ID Runs Label Doc
bqsr
bqsr.cwl (CommandLineTool)
create BQSR table
apply_bqsr
apply_bqsr.cwl (CommandLineTool)
apply BQSR
mark_duplicates_and_sort
mark_duplicates_and_sort.cwl (CommandLineTool)
mark duplicates and sort
bam_to_cram
bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
merge
merge.cwl (CommandLineTool)
merge BAMs
index_cram
index_cram.cwl (CommandLineTool)
samtools index cram
name_sort
name_sort.cwl (CommandLineTool)
sort BAM by name
align
align.cwl (Workflow)
Unaligned to aligned BAM

Outputs

ID Type Label Doc
final_cram File
mark_duplicates_metrics_file File
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/unaligned_bam_to_bqsr/workflow.cwl