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Graph	Name	Retrieved From	View
	somatic_exome: exome alignment and somatic variant detection somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome.cwl Branch/Commit ID: 74647cc0f1abac4ee22950cfa89c44cf2ca3cffd
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 74647cc0f1abac4ee22950cfa89c44cf2ca3cffd
	gatk4W.cwl Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using GATK4. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.	https://github.com/ambarishK/bio-cwl-tools.git Path: gatk4W.cwl Branch/Commit ID: 690ff2fa1ef356c42003e4b9986d39f4e44806a8
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 74647cc0f1abac4ee22950cfa89c44cf2ca3cffd
	wgs-processing-wf.cwl	https://github.com/arvados/arvados-tutorial.git Path: WGS-processing/cwl/wgs-processing-wf.cwl Branch/Commit ID: 36de0d12e1cc88d0fd7d6b401df6c6e403f8c809
	WGS processing workflow scattered over samples	https://github.com/arvados/arvados-tutorial.git Path: WGS-processing/cwl/wgs-processing-wf.cwl Branch/Commit ID: b50ffeeeae865d0780ca03c5a3f5065eeeb758e4
	WGS processing workflow for single sample	https://github.com/arvados/arvados-tutorial.git Path: WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl Branch/Commit ID: b50ffeeeae865d0780ca03c5a3f5065eeeb758e4
	bwamem-gatk-report-wf.cwl	https://github.com/arvados/arvados-tutorial.git Path: WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl Branch/Commit ID: 36de0d12e1cc88d0fd7d6b401df6c6e403f8c809
	gatk4W-spark.cwl Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using GATK4. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.	https://github.com/ambarishK/bio-cwl-tools.git Path: gatk4W-spark.cwl Branch/Commit ID: fcab170f3e8a4bc70601650401cce2a9df42f484
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 3bb0693076adc1543079a6b136c74906ad546ac6