3 label: Variant calling workflow for single interval
6 - class: SubworkflowFeatureRequirement
11 format: edam:format_2572 # BAM
12 label: Indexed sorted BAM with labeled duplicates
17 format: edam:format_1929 # FASTA
18 label: Reference genome
32 format: edam:format_3016 # VCF
33 label: VCF of known polymorphic sites for BQSR
38 label: Scatter intervals file
43 format: edam:format_3016 # GVCF
44 label: single interval filtered GVCF
45 outputSource: selectvariants/filteredgvcf
49 run: gatk-baserecalibrator-with-interval.cwl
54 knownsites1: knownsites1
55 intervallist: intervallist
58 run: gatk-applyBSQR-with-interval.cwl
63 intervallist: intervallist
64 recaltable: basecalibrator/recaltable
67 run: gatk-haplotypecaller-with-interval.cwl
70 bam: applyBQSR/recalbam
72 intervallist: intervallist
75 run: gatk-selectvariants.cwl
77 gvcf: haplotypecaller/gvcf
82 s:codeRepository: https://github.com/arvados/arvados-tutorial
83 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
86 s: https://schema.org/
87 edam: http://edamontology.org/
90 - https://schema.org/version/latest/schema.rdf
91 - http://edamontology.org/EDAM_1.18.owl