3 label: Variant calling workflow for given interval
6 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 format: edam:format_3016 # VCF
39 label: VCF of known polymorphic sites for BQSR
44 label: Scatter intervals file
49 format: edam:format_3016 # GVCF
50 label: Given interval filtered GVCF
51 outputSource: selectvariants/filteredgvcf
55 run: gatk-baserecalibrator-with-interval.cwl
60 knownsites1: knownsites1
61 knownsites2: knownsites2
62 intervallist: intervallist
65 run: gatk-applyBSQR-with-interval.cwl
70 intervallist: intervallist
71 recaltable: basecalibrator/recaltable
74 run: gatk-haplotypecaller-with-interval.cwl
77 bam: applyBQSR/recalbam
79 intervallist: intervallist
82 run: gatk-selectvariants.cwl
84 gvcf: haplotypecaller/gvcf
89 s:codeRepository: https://github.com/arvados/arvados-tutorial
90 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
93 s: https://schema.org/
94 edam: http://edamontology.org/
97 # - https://schema.org/version/latest/schema.rdf
98 # - http://edamontology.org/EDAM_1.18.owl