Mercurial > repos > iuc > cnv_vcf2json
comparison test-data/output.json @ 1:7d2d2e3b9891 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d
| author | iuc |
|---|---|
| date | Wed, 24 Jul 2024 12:56:03 +0000 |
| parents | c8caf812d33b |
| children |
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| 0:c8caf812d33b | 1:7d2d2e3b9891 |
|---|---|
| 1 [ | 1 [ |
| 2 { | 2 { |
| 3 "biosampleId": "HG00096", | 3 "biosampleId": "HG00096", |
| 4 "assemblyId": "GRCh38", | 4 "assemblyId": "GRCh38", |
| 5 "variantInternalId": "chr1:2650427-2651463:EFO:0030069", | 5 "variantInternalId": "chr1:2650427-2651463:EFO:0030069", |
| 6 "variantType": "DEL", | 6 "variantState": { |
| 7 "variantId": "EFO:0030069", | 7 "id": "EFO:0030069", |
| 8 "start": 2650427, | 8 "label": "complete genomic loss" |
| 9 "end": 2651463, | 9 }, |
| 10 "referenceName": "1", | 10 "definitions": { |
| 11 "Location": { | |
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| 13 "end": 2651463, | |
| 14 "chromosome": "1" | |
| 15 } | |
| 16 }, | |
| 11 "info": { | 17 "info": { |
| 12 "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463", | 18 "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463", |
| 13 "cnCount": 0, | 19 "cnCount": 0, |
| 14 "cnValue": 1.00369e-09 | 20 "cnValue": 1.00369e-09 |
| 15 } | 21 }, |
| 22 "updated": "2024-07-24T09:24:38.692461" | |
| 16 }, | 23 }, |
| 17 { | 24 { |
| 18 "biosampleId": "HG00096", | 25 "biosampleId": "HG00096", |
| 19 "assemblyId": "GRCh38", | 26 "assemblyId": "GRCh38", |
| 20 "variantInternalId": "chr1:2651463-2653075:EFO:0030068", | 27 "variantInternalId": "chr1:2651463-2653075:EFO:0030068", |
| 21 "variantType": "DEL", | 28 "variantState": { |
| 22 "variantId": "EFO:0030068", | 29 "id": "EFO:0030068", |
| 23 "start": 2651463, | 30 "label": "low-level loss" |
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| 25 "referenceName": "1", | 32 "definitions": { |
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| 35 "end": 2653075, | |
| 36 "chromosome": "1" | |
| 37 } | |
| 38 }, | |
| 26 "info": { | 39 "info": { |
| 27 "legacyId": "DRAGEN:LOSS:chr1:2651464-2653075", | 40 "legacyId": "DRAGEN:LOSS:chr1:2651464-2653075", |
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| 29 "cnValue": 0.395524 | 42 "cnValue": 0.395524 |
| 30 } | 43 }, |
| 44 "updated": "2024-07-24T09:24:38.692482" | |
| 31 }, | 45 }, |
| 32 { | 46 { |
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| 34 "assemblyId": "GRCh38", | 48 "assemblyId": "GRCh38", |
| 35 "variantInternalId": "chr1:4063594-4067475:EFO:0030068", | 49 "variantInternalId": "chr1:4063594-4067475:EFO:0030068", |
| 36 "variantType": "DEL", | 50 "variantState": { |
| 37 "variantId": "EFO:0030068", | 51 "id": "EFO:0030068", |
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| 58 "chromosome": "1" | |
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| 43 "cnCount": 1, | 63 "cnCount": 1, |
| 44 "cnValue": 0.429788 | 64 "cnValue": 0.429788 |
| 45 } | 65 }, |
| 66 "updated": "2024-07-24T09:24:38.692495" | |
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| 47 { | 68 { |
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| 49 "assemblyId": "GRCh38", | 70 "assemblyId": "GRCh38", |
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| 51 "variantType": "DEL", | 72 "variantState": { |
| 52 "variantId": "EFO:0030068", | 73 "id": "EFO:0030068", |
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| 80 "chromosome": "1" | |
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| 82 }, | |
| 56 "info": { | 83 "info": { |
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| 59 "cnValue": 0.543097 | 86 "cnValue": 0.543097 |
| 60 } | 87 }, |
| 88 "updated": "2024-07-24T09:24:38.692503" | |
| 61 }, | 89 }, |
| 62 { | 90 { |
| 63 "biosampleId": "HG00096", | 91 "biosampleId": "HG00096", |
| 64 "assemblyId": "GRCh38", | 92 "assemblyId": "GRCh38", |
| 65 "variantInternalId": "chr1:8143311-8150440:EFO:0030071", | 93 "variantInternalId": "chr1:8143311-8150440:EFO:0030071", |
| 66 "variantType": "DUP", | 94 "variantState": { |
| 67 "variantId": "EFO:0030071", | 95 "id": "EFO:0030071", |
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| 103 } | |
| 104 }, | |
| 71 "info": { | 105 "info": { |
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| 74 "cnValue": 1.42495 | 108 "cnValue": 1.42495 |
| 75 } | 109 }, |
| 110 "updated": "2024-07-24T09:24:38.692512" | |
| 76 }, | 111 }, |
| 77 { | 112 { |
| 78 "biosampleId": "HG00096", | 113 "biosampleId": "HG00096", |
| 79 "assemblyId": "GRCh38", | 114 "assemblyId": "GRCh38", |
| 80 "variantInternalId": "chr1:13224579-13242034:EFO:0030071", | 115 "variantInternalId": "chr1:13224579-13242034:EFO:0030071", |
| 81 "variantType": "DUP", | 116 "variantState": { |
| 82 "variantId": "EFO:0030071", | 117 "id": "EFO:0030071", |
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| 85 "referenceName": "1", | 120 "definitions": { |
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| 124 "chromosome": "1" | |
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| 126 }, | |
| 86 "info": { | 127 "info": { |
| 87 "legacyId": "DRAGEN:GAIN:chr1:13224580-13242034", | 128 "legacyId": "DRAGEN:GAIN:chr1:13224580-13242034", |
| 88 "cnCount": 3, | 129 "cnCount": 3, |
| 89 "cnValue": 1.49181 | 130 "cnValue": 1.49181 |
| 90 } | 131 }, |
| 91 }, | 132 "updated": "2024-07-24T09:24:38.692520" |
| 92 { | 133 }, |
| 93 "biosampleId": "HG00096", | 134 { |
| 94 "assemblyId": "GRCh38", | 135 "biosampleId": "HG00096", |
| 95 "variantInternalId": "chr1:16605061-16646293:EFO:0030071", | 136 "assemblyId": "GRCh38", |
| 96 "variantType": "DUP", | 137 "variantInternalId": "chr1:16605061-16646293:EFO:0030072", |
| 97 "variantId": "EFO:0030071", | 138 "variantState": { |
| 98 "start": 16605061, | 139 "id": "EFO:0030072", |
| 99 "end": 16646293, | 140 "label": "high-level gain" |
| 100 "referenceName": "1", | 141 }, |
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| 146 "chromosome": "1" | |
| 147 } | |
| 148 }, | |
| 101 "info": { | 149 "info": { |
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| 103 "cnCount": 7, | 151 "cnCount": 7, |
| 104 "cnValue": 3.3289 | 152 "cnValue": 3.3289 |
| 105 } | 153 }, |
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| 107 { | 155 }, |
| 108 "biosampleId": "HG00096", | 156 { |
| 109 "assemblyId": "GRCh38", | 157 "biosampleId": "HG00096", |
| 110 "variantInternalId": "chr1:16716711-16728256:EFO:0030071", | 158 "assemblyId": "GRCh38", |
| 111 "variantType": "DUP", | 159 "variantInternalId": "chr1:16716711-16728256:EFO:0030072", |
| 112 "variantId": "EFO:0030071", | 160 "variantState": { |
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| 114 "end": 16728256, | 162 "label": "high-level gain" |
| 115 "referenceName": "1", | 163 }, |
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| 168 "chromosome": "1" | |
| 169 } | |
| 170 }, | |
| 116 "info": { | 171 "info": { |
| 117 "legacyId": "DRAGEN:GAIN:chr1:16716712-16728256", | 172 "legacyId": "DRAGEN:GAIN:chr1:16716712-16728256", |
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| 119 "cnValue": 2.68822 | 174 "cnValue": 2.68822 |
| 120 } | 175 }, |
| 176 "updated": "2024-07-24T09:24:38.692539" | |
| 121 }, | 177 }, |
| 122 { | 178 { |
| 123 "biosampleId": "HG00096", | 179 "biosampleId": "HG00096", |
| 124 "assemblyId": "GRCh38", | 180 "assemblyId": "GRCh38", |
| 125 "variantInternalId": "chr1:16879751-16950196:EFO:0030071", | 181 "variantInternalId": "chr1:16879751-16950196:EFO:0030071", |
| 126 "variantType": "DUP", | 182 "variantState": { |
| 127 "variantId": "EFO:0030071", | 183 "id": "EFO:0030071", |
| 128 "start": 16879751, | 184 "label": "low-level gain" |
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| 192 }, | |
| 131 "info": { | 193 "info": { |
| 132 "legacyId": "DRAGEN:GAIN:chr1:16879752-16950196", | 194 "legacyId": "DRAGEN:GAIN:chr1:16879752-16950196", |
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| 134 "cnValue": 1.53152 | 196 "cnValue": 1.53152 |
| 135 } | 197 }, |
| 198 "updated": "2024-07-24T09:24:38.692546" | |
| 136 }, | 199 }, |
| 137 { | 200 { |
| 138 "biosampleId": "HG00096", | 201 "biosampleId": "HG00096", |
| 139 "assemblyId": "GRCh38", | 202 "assemblyId": "GRCh38", |
| 140 "variantInternalId": "chr1:34636777-34646300:EFO:0030068", | 203 "variantInternalId": "chr1:34636777-34646300:EFO:0030068", |
| 141 "variantType": "DEL", | 204 "variantState": { |
| 142 "variantId": "EFO:0030068", | 205 "id": "EFO:0030068", |
| 143 "start": 34636777, | 206 "label": "low-level loss" |
| 144 "end": 34646300, | 207 }, |
| 145 "referenceName": "1", | 208 "definitions": { |
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| 214 }, | |
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| 149 "cnValue": 0.495288 | 218 "cnValue": 0.495288 |
| 150 } | 219 }, |
| 220 "updated": "2024-07-24T09:24:38.692554" | |
| 151 }, | 221 }, |
| 152 { | 222 { |
| 153 "biosampleId": "HG00096", | 223 "biosampleId": "HG00096", |
| 154 "assemblyId": "GRCh38", | 224 "assemblyId": "GRCh38", |
| 155 "variantInternalId": "chr1:36957723-36960386:EFO:0030068", | 225 "variantInternalId": "chr1:36957723-36960386:EFO:0030068", |
| 156 "variantType": "DEL", | 226 "variantState": { |
| 157 "variantId": "EFO:0030068", | 227 "id": "EFO:0030068", |
| 158 "start": 36957723, | 228 "label": "low-level loss" |
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| 236 }, | |
| 161 "info": { | 237 "info": { |
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| 164 "cnValue": 0.479029 | 240 "cnValue": 0.479029 |
| 165 } | 241 }, |
| 242 "updated": "2024-07-24T09:24:38.692561" | |
| 166 }, | 243 }, |
| 167 { | 244 { |
| 168 "biosampleId": "HG00096", | 245 "biosampleId": "HG00096", |
| 169 "assemblyId": "GRCh38", | 246 "assemblyId": "GRCh38", |
| 170 "variantInternalId": "chr1:43593157-43594353:EFO:0030068", | 247 "variantInternalId": "chr1:43593157-43594353:EFO:0030068", |
| 171 "variantType": "DEL", | 248 "variantState": { |
| 172 "variantId": "EFO:0030068", | 249 "id": "EFO:0030068", |
| 173 "start": 43593157, | 250 "label": "low-level loss" |
| 174 "end": 43594353, | 251 }, |
| 175 "referenceName": "1", | 252 "definitions": { |
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| 256 "chromosome": "1" | |
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| 258 }, | |
| 176 "info": { | 259 "info": { |
| 177 "legacyId": "DRAGEN:LOSS:chr1:43593158-43594353", | 260 "legacyId": "DRAGEN:LOSS:chr1:43593158-43594353", |
| 178 "cnCount": 1, | 261 "cnCount": 1, |
| 179 "cnValue": 0.289679 | 262 "cnValue": 0.289679 |
| 180 } | 263 }, |
| 264 "updated": "2024-07-24T09:24:38.692568" | |
| 181 }, | 265 }, |
| 182 { | 266 { |
| 183 "biosampleId": "HG00096", | 267 "biosampleId": "HG00096", |
| 184 "assemblyId": "GRCh38", | 268 "assemblyId": "GRCh38", |
| 185 "variantInternalId": "chr1:58278107-58279217:EFO:0030069", | 269 "variantInternalId": "chr1:58278107-58279217:EFO:0030069", |
| 186 "variantType": "DEL", | 270 "variantState": { |
| 187 "variantId": "EFO:0030069", | 271 "id": "EFO:0030069", |
| 188 "start": 58278107, | 272 "label": "complete genomic loss" |
| 189 "end": 58279217, | 273 }, |
| 190 "referenceName": "1", | 274 "definitions": { |
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| 277 "end": 58279217, | |
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| 279 } | |
| 280 }, | |
| 191 "info": { | 281 "info": { |
| 192 "legacyId": "DRAGEN:LOSS:chr1:58278108-58279217", | 282 "legacyId": "DRAGEN:LOSS:chr1:58278108-58279217", |
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| 194 "cnValue": 0.0937719 | 284 "cnValue": 0.0937719 |
| 195 } | 285 }, |
| 286 "updated": "2024-07-24T09:24:38.692575" | |
| 196 }, | 287 }, |
| 197 { | 288 { |
| 198 "biosampleId": "HG00096", | 289 "biosampleId": "HG00096", |
| 199 "assemblyId": "GRCh38", | 290 "assemblyId": "GRCh38", |
| 200 "variantInternalId": "chr1:61647700-61655464:EFO:0030068", | 291 "variantInternalId": "chr1:61647700-61655464:EFO:0030068", |
| 201 "variantType": "DEL", | 292 "variantState": { |
| 202 "variantId": "EFO:0030068", | 293 "id": "EFO:0030068", |
| 203 "start": 61647700, | 294 "label": "low-level loss" |
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| 205 "referenceName": "1", | 296 "definitions": { |
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| 300 "chromosome": "1" | |
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| 302 }, | |
| 206 "info": { | 303 "info": { |
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| 209 "cnValue": 0.52381 | 306 "cnValue": 0.52381 |
| 210 } | 307 }, |
| 308 "updated": "2024-07-24T09:24:38.692589" | |
| 211 }, | 309 }, |
| 212 { | 310 { |
| 213 "biosampleId": "HG00096", | 311 "biosampleId": "HG00096", |
| 214 "assemblyId": "GRCh38", | 312 "assemblyId": "GRCh38", |
| 215 "variantInternalId": "chr1:62188614-62191346:EFO:0030068", | 313 "variantInternalId": "chr1:62188614-62191346:EFO:0030068", |
| 216 "variantType": "DEL", | 314 "variantState": { |
| 217 "variantId": "EFO:0030068", | 315 "id": "EFO:0030068", |
| 218 "start": 62188614, | 316 "label": "low-level loss" |
| 219 "end": 62191346, | 317 }, |
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| 322 "chromosome": "1" | |
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| 324 }, | |
| 221 "info": { | 325 "info": { |
| 222 "legacyId": "DRAGEN:LOSS:chr1:62188615-62191346", | 326 "legacyId": "DRAGEN:LOSS:chr1:62188615-62191346", |
| 223 "cnCount": 1, | 327 "cnCount": 1, |
| 224 "cnValue": 0.483858 | 328 "cnValue": 0.483858 |
| 225 } | 329 }, |
| 330 "updated": "2024-07-24T09:24:38.692597" | |
| 226 }, | 331 }, |
| 227 { | 332 { |
| 228 "biosampleId": "HG00096", | 333 "biosampleId": "HG00096", |
| 229 "assemblyId": "GRCh38", | 334 "assemblyId": "GRCh38", |
| 230 "variantInternalId": "chr1:67542030-67543275:EFO:0030069", | 335 "variantInternalId": "chr1:67542030-67543275:EFO:0030069", |
| 231 "variantType": "DEL", | 336 "variantState": { |
| 232 "variantId": "EFO:0030069", | 337 "id": "EFO:0030069", |
| 233 "start": 67542030, | 338 "label": "complete genomic loss" |
| 234 "end": 67543275, | 339 }, |
| 235 "referenceName": "1", | 340 "definitions": { |
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| 343 "end": 67543275, | |
| 344 "chromosome": "1" | |
| 345 } | |
| 346 }, | |
| 236 "info": { | 347 "info": { |
| 237 "legacyId": "DRAGEN:LOSS:chr1:67542031-67543275", | 348 "legacyId": "DRAGEN:LOSS:chr1:67542031-67543275", |
| 238 "cnCount": 0, | 349 "cnCount": 0, |
| 239 "cnValue": 0.0312573 | 350 "cnValue": 0.0312573 |
| 240 } | 351 }, |
| 352 "updated": "2024-07-24T09:24:38.692603" | |
| 241 }, | 353 }, |
| 242 { | 354 { |
| 243 "biosampleId": "HG00096", | 355 "biosampleId": "HG00096", |
| 244 "assemblyId": "GRCh38", | 356 "assemblyId": "GRCh38", |
| 245 "variantInternalId": "chr1:72289205-72345923:EFO:0030068", | 357 "variantInternalId": "chr1:72289205-72345923:EFO:0030068", |
| 246 "variantType": "DEL", | 358 "variantState": { |
| 247 "variantId": "EFO:0030068", | 359 "id": "EFO:0030068", |
| 248 "start": 72289205, | 360 "label": "low-level loss" |
| 249 "end": 72345923, | 361 }, |
| 250 "referenceName": "1", | 362 "definitions": { |
| 363 "Location": { | |
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| 365 "end": 72345923, | |
| 366 "chromosome": "1" | |
| 367 } | |
| 368 }, | |
| 251 "info": { | 369 "info": { |
| 252 "legacyId": "DRAGEN:LOSS:chr1:72289206-72345923", | 370 "legacyId": "DRAGEN:LOSS:chr1:72289206-72345923", |
| 253 "cnCount": 1, | 371 "cnCount": 1, |
| 254 "cnValue": 0.486641 | 372 "cnValue": 0.486641 |
| 255 } | 373 }, |
| 374 "updated": "2024-07-24T09:24:38.692610" | |
| 256 }, | 375 }, |
| 257 { | 376 { |
| 258 "biosampleId": "HG00096", | 377 "biosampleId": "HG00096", |
| 259 "assemblyId": "GRCh38", | 378 "assemblyId": "GRCh38", |
| 260 "variantInternalId": "chr1:78183859-78192785:EFO:0030068", | 379 "variantInternalId": "chr1:78183859-78192785:EFO:0030068", |
| 261 "variantType": "DEL", | 380 "variantState": { |
| 262 "variantId": "EFO:0030068", | 381 "id": "EFO:0030068", |
| 263 "start": 78183859, | 382 "label": "low-level loss" |
| 264 "end": 78192785, | 383 }, |
| 265 "referenceName": "1", | 384 "definitions": { |
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| 388 "chromosome": "1" | |
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