{"@id":"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl","retrievedFrom":{"repoUrl":"https://github.com/Duke-GCB/bespin-cwl.git","branch":"68c92437c854a200433ee684067f81f13de5d8eb","path":"packed/exomeseq.cwl","packedId":"exomeseq-02-variantdiscovery.cwl","type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/Duke-GCB/bespin-cwl/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl","url":"https://github.com/Duke-GCB/bespin-cwl/blob/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl"},"retrievedOn":"2024-05-09T14:23:28.630+00:00","lastCommit":"68c92437c854a200433ee684067f81f13de5d8eb","label":"exomeseq.cwl#exomeseq-02-variantdiscovery.cwl","inputs":{"name":{"type":"String"},"GATKJar":{"type":"File"},"threads":{"type":"Integer (Optional)"},"intervals":{"type":"File[] (Optional)"},"study_type":{"type":"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#bespin-types.yml/ExomeseqStudyType"},"raw_variants":{"type":"File[]"},"resource_dbsnp":{"type":"File"},"interval_padding":{"type":"Integer (Optional)"},"reference_genome":{"type":"File"},"snp_resource_1kg":{"type":"File"},"snp_resource_omni":{"type":"File"},"snp_resource_hapmap":{"type":"File"},"indel_resource_mills":{"type":"File"}},"outputs":{"joint_raw_variants":{"doc":"VCF file from joint genotyping calling","type":"File"},"variant_recalibration_snps_vcf":{"doc":"The output filtered and recalibrated VCF file in SNP mode in which each variant is annotated with its VQSLOD value","type":"File"},"variant_recalibration_snps_recal":{"doc":"The output recal file used by ApplyRecalibration in SNP mode","type":"File"},"variant_recalibration_snps_rscript":{"doc":"The output rscript file generated by the VQSR in SNP mode to aid in visualization of the input data and learned model","type":"File"},"variant_recalibration_snps_tranches":{"doc":"The output tranches file used by ApplyRecalibration in SNP mode","type":"File"},"variant_recalibration_snps_indels_vcf":{"doc":"The output filtered and recalibrated VCF file in in which each variant is annotated with its VQSLOD value","type":"File"},"variant_recalibration_snps_indels_recal":{"doc":"The output recal file used by ApplyRecalibration in INDEL mode","type":"File"},"variant_recalibration_snps_indels_rscript":{"doc":"The output rscript file generated by the VQSR in INDEL mode to aid in visualization of the input data and learned model","type":"File"},"variant_recalibration_snps_indels_tranches":{"doc":"The output tranches file used by ApplyRecalibration in INDEL mode","type":"File"}},"steps":{"joint_genotyping":{"doc":"GATK-GenotypeGVCFs.cwl is developed for CWL consortium\nPerform joint genotyping on gVCF files produced by HaplotypeCaller\n","run":"exomeseq.cwl#GATK-GenotypeGVCFs.cwl","runType":"COMMANDLINETOOL","sources":{"joint_genotyping":{"sourceIDs":["interval_padding"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/dbsnp":{"sourceIDs":["resource_dbsnp"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/group":{"defaultVal":"\\\"StandardAnnotation\\\""},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/GATKJar":{"sourceIDs":["GATKJar"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/threads":{"defaultVal":"1"},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/variants":{"sourceIDs":["raw_variants"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/intervals":{"sourceIDs":["intervals"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/reference":{"sourceIDs":["reference_genome"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/joint_genotyping/outputfile_GenotypeGVCFs":{"sourceIDs":["generate_joint_filenames"]}}},"apply_recalibration_snps":{"run":"exomeseq.cwl#GATK-ApplyRecalibration.cwl","runType":"COMMANDLINETOOL","sources":{"apply_recalibration_snps":{"sourceIDs":["reference_genome"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/mode":{"defaultVal":"\\\"SNP\\\""},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/GATKJar":{"sourceIDs":["GATKJar"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/threads":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/variants":{"sourceIDs":["joint_genotyping"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/recal_file":{"sourceIDs":["variant_recalibration_snps"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/tranches_file":{"sourceIDs":["variant_recalibration_snps"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/ts_filter_level":{"defaultVal":"9.9e+01"},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_snps/outputfile_recalibrated_vcf":{"sourceIDs":["generate_joint_filenames"]}}},"generate_joint_filenames":{"label":"Generates a set of file names for joint steps based on an input name","run":"exomeseq.cwl#generate-joint-filenames.cwl","runType":"EXPRESSIONTOOL","sources":{"generate_joint_filenames":{"sourceIDs":["name"]}}},"generate_annotations_snps":{"label":"Given an ExomeseqStudyType returns an array of the annotations to use.","doc":"The InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be computed. For projects with fewer samples, or that includes many closely related samples (such as a family) please omit this annotation from the command line. From https://software.broadinstitute.org/gatk/documentation/article?id=1259\n","run":"exomeseq.cwl#generate-variant-recalibration-annotation-set.cwl","runType":"EXPRESSIONTOOL","sources":{"generate_annotations_snps":{"sourceIDs":["study_type"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/generate_annotations_snps/base_annotations":{"defaultVal":"\\\"FS\\\""}}},"apply_recalibration_indels":{"run":"exomeseq.cwl#GATK-ApplyRecalibration.cwl","runType":"COMMANDLINETOOL","sources":{"apply_recalibration_indels":{"sourceIDs":["generate_joint_filenames"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/mode":{"defaultVal":"\\\"INDEL\\\""},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/GATKJar":{"sourceIDs":["GATKJar"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/threads":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/variants":{"sourceIDs":["apply_recalibration_snps"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/reference":{"sourceIDs":["reference_genome"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/recal_file":{"sourceIDs":["variant_recalibration_indels"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/tranches_file":{"sourceIDs":["variant_recalibration_indels"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/apply_recalibration_indels/ts_filter_level":{"defaultVal":"9.9e+01"}}},"variant_recalibration_snps":{"doc":"GATK-VariantsRecalibrator.cwl is developed for CWL consortium\n\nUsage:\n```\njava -Xmx8G \\\n      -jar gatk.jar\n      -T VariantRecalibrator \\\n      -R [reference_fasta] \\\n      -recalFile    $tmpDir/out.recal \\\n      -tranchesFile $tmpDir/out.tranches \\\n      -rscriptFile  $tmpDir/out.R \\\n      -nt 4 \\\n      -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \\\n      -mode SNP \\\n      -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \\\n      -resource:dbsnp,known=true,training=false,truth=false,prior=2.0  [dbsnp_vcf] \\\n      -resource:omni,known=false,training=true,truth=true,prior=12.0   [1komni_vcf] \\\n      -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf]\n```\n","run":"exomeseq.cwl#GATK-VariantRecalibrator-SNPs.cwl","runType":"COMMANDLINETOOL","sources":{"variant_recalibration_snps":{"defaultVal":"1"},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/GATKJar":{"sourceIDs":["GATKJar"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/variants":{"sourceIDs":["joint_genotyping"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/reference":{"sourceIDs":["reference_genome"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/annotations":{"sourceIDs":["generate_annotations_snps"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/resource_1kg":{"sourceIDs":["snp_resource_1kg"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/resource_omni":{"sourceIDs":["snp_resource_omni"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/resource_dbsnp":{"sourceIDs":["resource_dbsnp"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/resource_hapmap":{"sourceIDs":["snp_resource_hapmap"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/outputfile_recal":{"sourceIDs":["generate_joint_filenames"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/outputfile_rscript":{"sourceIDs":["generate_joint_filenames"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_snps/outputfile_tranches":{"sourceIDs":["generate_joint_filenames"]}}},"generate_annotations_indels":{"label":"Given an ExomeseqStudyType returns an array of the annotations to use.","doc":"The InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be computed. For projects with fewer samples, or that includes many closely related samples (such as a family) please omit this annotation from the command line. From https://software.broadinstitute.org/gatk/documentation/article?id=1259\n","run":"exomeseq.cwl#generate-variant-recalibration-annotation-set.cwl","runType":"EXPRESSIONTOOL","sources":{"generate_annotations_indels":{"sourceIDs":["study_type"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/generate_annotations_indels/base_annotations":{"defaultVal":"\\\"FS\\\""}}},"variant_recalibration_indels":{"doc":"GATK-VariantsRecalibrator.cwl is developed for CWL consortium\n\nUsage:\n```\njava -Xmx8G \\\n      -jar gatk.jar\n      -T VariantRecalibrator \\\n      -R [reference_fasta] \\\n      -recalFile    $tmpDir/out.recal \\\n      -tranchesFile $tmpDir/out.tranches \\\n      -rscriptFile  $tmpDir/out.R \\\n      -nt 4 \\\n      -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \\\n      -mode SNP \\\n      -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \\\n      -resource:dbsnp,known=true,training=false,truth=false,prior=2.0  [dbsnp_vcf] \\\n      -resource:omni,known=false,training=true,truth=true,prior=12.0   [1komni_vcf] \\\n      -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf]\n```\n","run":"exomeseq.cwl#GATK-VariantRecalibrator-Indels.cwl","runType":"COMMANDLINETOOL","sources":{"variant_recalibration_indels":{"sourceIDs":["generate_annotations_indels"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/GATKJar":{"sourceIDs":["GATKJar"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/threads":{"defaultVal":"1"},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/variants":{"sourceIDs":["apply_recalibration_snps"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/reference":{"sourceIDs":["reference_genome"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/resource_dbsnp":{"sourceIDs":["resource_dbsnp"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/resource_mills":{"sourceIDs":["indel_resource_mills"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/outputfile_recal":{"sourceIDs":["generate_joint_filenames"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/outputfile_rscript":{"sourceIDs":["generate_joint_filenames"]},"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#exomeseq-02-variantdiscovery.cwl/variant_recalibration_indels/outputfile_tranches":{"sourceIDs":["generate_joint_filenames"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"snp_resource_hapmap\" [fillcolor=\"#94DDF4\",label=\"snp_resource_hapmap\"];\n    \"intervals\" [fillcolor=\"#94DDF4\",label=\"intervals\"];\n    \"interval_padding\" [fillcolor=\"#94DDF4\",label=\"interval_padding\"];\n    \"indel_resource_mills\" [fillcolor=\"#94DDF4\",label=\"indel_resource_mills\"];\n    \"snp_resource_omni\" [fillcolor=\"#94DDF4\",label=\"snp_resource_omni\"];\n    \"reference_genome\" [fillcolor=\"#94DDF4\",label=\"reference_genome\"];\n    \"resource_dbsnp\" [fillcolor=\"#94DDF4\",label=\"resource_dbsnp\"];\n    \"GATKJar\" [fillcolor=\"#94DDF4\",label=\"GATKJar\"];\n    \"threads\" [fillcolor=\"#94DDF4\",label=\"threads\"];\n    \"snp_resource_1kg\" [fillcolor=\"#94DDF4\",label=\"snp_resource_1kg\"];\n    \"study_type\" [fillcolor=\"#94DDF4\",label=\"study_type\"];\n    \"name\" [fillcolor=\"#94DDF4\",label=\"name\"];\n    \"raw_variants\" [fillcolor=\"#94DDF4\",label=\"raw_variants\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"variant_recalibration_snps_tranches\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_tranches\"];\n    \"joint_raw_variants\" [fillcolor=\"#94DDF4\",label=\"joint_raw_variants\"];\n    \"variant_recalibration_snps_indels_tranches\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_indels_tranches\"];\n    \"variant_recalibration_snps_indels_recal\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_indels_recal\"];\n    \"variant_recalibration_snps_vcf\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_vcf\"];\n    \"variant_recalibration_snps_rscript\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_rscript\"];\n    \"variant_recalibration_snps_indels_vcf\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_indels_vcf\"];\n    \"variant_recalibration_snps_indels_rscript\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_indels_rscript\"];\n    \"variant_recalibration_snps_recal\" [fillcolor=\"#94DDF4\",label=\"variant_recalibration_snps_recal\"];\n  }\n  \"generate_annotations_snps\" [label=\"Given an ExomeseqStudyType returns an array of the annotations to use.\"];\n  \"variant_recalibration_snps\" [label=\"variant_recalibration_snps\"];\n  \"apply_recalibration_snps\" [label=\"apply_recalibration_snps\"];\n  \"joint_genotyping\" [label=\"joint_genotyping\"];\n  \"apply_recalibration_indels\" [label=\"apply_recalibration_indels\"];\n  \"variant_recalibration_indels\" [label=\"variant_recalibration_indels\"];\n  \"generate_annotations_indels\" [label=\"Given an ExomeseqStudyType returns an array of the annotations to use.\"];\n  \"generate_joint_filenames\" [label=\"Generates a set of file names for joint steps based on an input name\"];\n  \"study_type\" -> \"generate_annotations_snps\" [label=\"study_type\"];\n  \"default1\" -> \"generate_annotations_snps\" [label=\"base_annotations\"];\n  \"default1\" [label=\"\\\"SOR\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default2\" -> \"generate_annotations_snps\" [label=\"base_annotations\"];\n  \"default2\" [label=\"\\\"ReadPosRankSum\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default3\" -> \"generate_annotations_snps\" [label=\"base_annotations\"];\n  \"default3\" [label=\"\\\"QD\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default4\" -> \"generate_annotations_snps\" [label=\"base_annotations\"];\n  \"default4\" [label=\"\\\"MQRankSum\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default5\" -> \"generate_annotations_snps\" [label=\"base_annotations\"];\n  \"default5\" [label=\"\\\"MQ\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default6\" -> \"generate_annotations_snps\" [label=\"base_annotations\"];\n  \"default6\" [label=\"\\\"FS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default7\" -> \"variant_recalibration_snps\" [label=\"threads\"];\n  \"default7\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"generate_joint_filenames\" -> \"variant_recalibration_snps\" [label=\"outputfile_rscript\"];\n  \"snp_resource_omni\" -> \"variant_recalibration_snps\" [label=\"resource_omni\"];\n  \"resource_dbsnp\" -> \"variant_recalibration_snps\" [label=\"resource_dbsnp\"];\n  \"snp_resource_1kg\" -> \"variant_recalibration_snps\" [label=\"resource_1kg\"];\n  \"joint_genotyping\" -> \"variant_recalibration_snps\" [label=\"variants\"];\n  \"generate_joint_filenames\" -> \"variant_recalibration_snps\" [label=\"outputfile_tranches\"];\n  \"generate_joint_filenames\" -> \"variant_recalibration_snps\" [label=\"outputfile_recal\"];\n  \"snp_resource_hapmap\" -> \"variant_recalibration_snps\" [label=\"resource_hapmap\"];\n  \"reference_genome\" -> \"variant_recalibration_snps\" [label=\"reference\"];\n  \"GATKJar\" -> \"variant_recalibration_snps\" [label=\"GATKJar\"];\n  \"generate_annotations_snps\" -> \"variant_recalibration_snps\" [label=\"annotations\"];\n  \"reference_genome\" -> \"apply_recalibration_snps\" [label=\"reference\"];\n  \"threads\" -> \"apply_recalibration_snps\" [label=\"threads\"];\n  \"generate_joint_filenames\" -> \"apply_recalibration_snps\" [label=\"outputfile_recalibrated_vcf\"];\n  \"variant_recalibration_snps\" -> \"apply_recalibration_snps\" [label=\"recal_file\"];\n  \"GATKJar\" -> \"apply_recalibration_snps\" [label=\"GATKJar\"];\n  \"default8\" -> \"apply_recalibration_snps\" [label=\"mode\"];\n  \"default8\" [label=\"\\\"SNP\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default9\" -> \"apply_recalibration_snps\" [label=\"ts_filter_level\"];\n  \"default9\" [label=\"9.9e+01\", fillcolor=\"#D5AEFC\"];\n  \"variant_recalibration_snps\" -> \"apply_recalibration_snps\" [label=\"tranches_file\"];\n  \"joint_genotyping\" -> \"apply_recalibration_snps\" [label=\"variants\"];\n  \"interval_padding\" -> \"joint_genotyping\" [label=\"interval_padding\"];\n  \"generate_joint_filenames\" -> \"joint_genotyping\" [label=\"outputfile_GenotypeGVCFs\"];\n  \"default10\" -> \"joint_genotyping\" [label=\"threads\"];\n  \"default10\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"resource_dbsnp\" -> \"joint_genotyping\" [label=\"dbsnp\"];\n  \"default11\" -> \"joint_genotyping\" [label=\"group\"];\n  \"default11\" [label=\"\\\"StandardAnnotation\\\"\", fillcolor=\"#D5AEFC\"];\n  \"raw_variants\" -> \"joint_genotyping\" [label=\"variants\"];\n  \"reference_genome\" -> \"joint_genotyping\" [label=\"reference\"];\n  \"intervals\" -> \"joint_genotyping\" [label=\"intervals\"];\n  \"GATKJar\" -> \"joint_genotyping\" [label=\"GATKJar\"];\n  \"generate_joint_filenames\" -> \"apply_recalibration_indels\" [label=\"outputfile_recalibrated_vcf\"];\n  \"variant_recalibration_indels\" -> \"apply_recalibration_indels\" [label=\"recal_file\"];\n  \"GATKJar\" -> \"apply_recalibration_indels\" [label=\"GATKJar\"];\n  \"default12\" -> \"apply_recalibration_indels\" [label=\"ts_filter_level\"];\n  \"default12\" [label=\"9.9e+01\", fillcolor=\"#D5AEFC\"];\n  \"variant_recalibration_indels\" -> \"apply_recalibration_indels\" [label=\"tranches_file\"];\n  \"default13\" -> \"apply_recalibration_indels\" [label=\"mode\"];\n  \"default13\" [label=\"\\\"INDEL\\\"\", fillcolor=\"#D5AEFC\"];\n  \"threads\" -> \"apply_recalibration_indels\" [label=\"threads\"];\n  \"reference_genome\" -> \"apply_recalibration_indels\" [label=\"reference\"];\n  \"apply_recalibration_snps\" -> \"apply_recalibration_indels\" [label=\"variants\"];\n  \"generate_annotations_indels\" -> \"variant_recalibration_indels\" [label=\"annotations\"];\n  \"default14\" -> \"variant_recalibration_indels\" [label=\"threads\"];\n  \"default14\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"reference_genome\" -> \"variant_recalibration_indels\" [label=\"reference\"];\n  \"apply_recalibration_snps\" -> \"variant_recalibration_indels\" [label=\"variants\"];\n  \"resource_dbsnp\" -> \"variant_recalibration_indels\" [label=\"resource_dbsnp\"];\n  \"GATKJar\" -> \"variant_recalibration_indels\" [label=\"GATKJar\"];\n  \"indel_resource_mills\" -> \"variant_recalibration_indels\" [label=\"resource_mills\"];\n  \"generate_joint_filenames\" -> \"variant_recalibration_indels\" [label=\"outputfile_tranches\"];\n  \"generate_joint_filenames\" -> \"variant_recalibration_indels\" [label=\"outputfile_recal\"];\n  \"generate_joint_filenames\" -> \"variant_recalibration_indels\" [label=\"outputfile_rscript\"];\n  \"study_type\" -> \"generate_annotations_indels\" [label=\"study_type\"];\n  \"default15\" -> \"generate_annotations_indels\" [label=\"base_annotations\"];\n  \"default15\" [label=\"\\\"ReadPosRankSum\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default16\" -> \"generate_annotations_indels\" [label=\"base_annotations\"];\n  \"default16\" [label=\"\\\"QD\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default17\" -> \"generate_annotations_indels\" [label=\"base_annotations\"];\n  \"default17\" [label=\"\\\"MQRankSum\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default18\" -> \"generate_annotations_indels\" [label=\"base_annotations\"];\n  \"default18\" [label=\"\\\"MQ\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default19\" -> \"generate_annotations_indels\" [label=\"base_annotations\"];\n  \"default19\" [label=\"\\\"FS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"name\" -> \"generate_joint_filenames\" [label=\"name\"];\n  \"variant_recalibration_snps\" -> \"variant_recalibration_snps_tranches\";\n  \"joint_genotyping\" -> \"joint_raw_variants\";\n  \"variant_recalibration_indels\" -> \"variant_recalibration_snps_indels_tranches\";\n  \"variant_recalibration_indels\" -> \"variant_recalibration_snps_indels_recal\";\n  \"apply_recalibration_snps\" -> \"variant_recalibration_snps_vcf\";\n  \"variant_recalibration_snps\" -> \"variant_recalibration_snps_rscript\";\n  \"apply_recalibration_indels\" -> \"variant_recalibration_snps_indels_vcf\";\n  \"variant_recalibration_indels\" -> \"variant_recalibration_snps_indels_rscript\";\n  \"variant_recalibration_snps\" -> \"variant_recalibration_snps_recal\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl?part=exomeseq-02-variantdiscovery.cwl","packed":true,"visualisationXdot":"/graph/xdot/github.com/Duke-GCB/bespin-cwl/blob/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl%23exomeseq-02-variantdiscovery.cwl","visualisationPng":"/graph/png/github.com/Duke-GCB/bespin-cwl/blob/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl%23exomeseq-02-variantdiscovery.cwl","visualisationSvg":"/graph/svg/github.com/Duke-GCB/bespin-cwl/blob/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl%23exomeseq-02-variantdiscovery.cwl","roBundle":"/robundle/github.com/Duke-GCB/bespin-cwl/blob/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl%23exomeseq-02-variantdiscovery.cwl","licenseName":"MIT License"}