3 label: Variant calling workflow scattered over interval splits
6 - class: SubworkflowFeatureRequirement
7 - class: ScatterFeatureRequirement
12 format: edam:format_2572 # BAM
13 label: Indexed sorted BAM with labeled duplicates
18 format: edam:format_1929 # FASTA
19 label: Reference genome
33 format: edam:format_3016 # VCF
34 label: VCF of known polymorphic sites for BQSR
39 label: Desired split for variant calling
44 format: edam:format_3016 # GVCF
45 label: GVCF generated from GATK Haplotype Caller
48 outputSource: merge-GVCFs/gatheredgvcf
52 run: gatk-splitintervals.cwl
56 scattercount: scattercount
59 recal-haplotypecaller:
60 run: gatk-wf-with-interval.cwl
66 knownsites1: knownsites1
67 intervallist: splitintervals/intervalfiles
71 run: gather-array-vcf.cwl
73 gvcfarray: recal-haplotypecaller/gvcf
78 s:codeRepository: https://github.com/arvados/arvados-tutorial
79 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
82 s: https://schema.org/
83 edam: http://edamontology.org/
86 - https://schema.org/version/latest/schema.rdf
87 - http://edamontology.org/EDAM_1.18.owl