annotate test-data/test_4.json @ 1:891283e0ee89 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
author bgruening
date Thu, 05 May 2022 20:27:17 +0000
parents d67642a21a1d
children
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0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
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1 [
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2 {
1
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3 "geneSymbol": "ABCG2",
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4 "chr": "chr4",
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5 "phased": true,
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6 "callSource": "MATCHER",
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7 "uncalledHaplotypes": [
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8 "rs2231142 reference (G)",
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9 "rs2231142 variant (T)"
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10 ],
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11 "messages": [],
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12 "relatedDrugs": [],
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13 "matcherDiplotypes": [
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14 {
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15 "allele1": {
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16 "gene": "ABCG2",
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17 "name": "Unknown",
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18 "function": "Unassigned function",
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19 "reference": false
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20 },
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21 "allele2": {
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22 "gene": "ABCG2",
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23 "name": "Unknown",
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24 "function": "Unassigned function",
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25 "reference": false
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26 },
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27 "gene": "ABCG2",
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28 "phenotypes": [
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29 "No Result"
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30 ],
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31 "variant": null,
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32 "lookupKey": [
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33 "No Result"
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34 ],
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35 "label": "Unknown/Unknown"
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36 }
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37 ],
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38 "diplotypes": [
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39 {
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40 "allele1": {
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41 "gene": "ABCG2",
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42 "name": "Unknown",
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43 "function": "Unassigned function",
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44 "reference": false
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45 },
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46 "allele2": {
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47 "gene": "ABCG2",
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48 "name": "Unknown",
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49 "function": "Unassigned function",
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50 "reference": false
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51 },
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52 "gene": "ABCG2",
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53 "phenotypes": [
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54 "No Result"
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55 ],
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56 "variant": null,
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57 "lookupKey": [
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58 "No Result"
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59 ],
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60 "label": "Unknown/Unknown"
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61 }
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62 ],
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63 "variants": [
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64 {
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65 "gene": "ABCG2",
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66 "chromosome": "chr4",
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67 "position": 88131171,
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68 "dbSnpId": "rs2231142",
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69 "call": null,
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70 "alleles": [
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71 "rs2231142 variant (T)"
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72 ],
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73 "phased": false,
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74 "wildtypeAllele": "G",
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75 "mismatch": false,
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76 "warnings": []
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77 }
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78 ],
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79 "variantsOfInterest": [],
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80 "highlightedVariants": []
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81 },
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82 {
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83 "geneSymbol": "CACNA1S",
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84 "chr": "chr1",
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85 "phased": true,
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86 "callSource": "MATCHER",
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87 "uncalledHaplotypes": [],
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88 "messages": [],
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89 "relatedDrugs": [],
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90 "matcherDiplotypes": [
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91 {
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92 "allele1": {
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148 "c.3257G\u003eA"
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168 }
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180 "relatedDrugs": [],
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184 "gene": "CFTR",
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1013 {
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1021 "*13"
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1036 ],
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1055 },
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1063 "*26"
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1064 ],
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1069 },
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1077 "*20"
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1078 ],
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1083 },
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1089 "call": "G|G",
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1091 "*6",
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1092 "*7",
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1093 "*9",
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1094 "*13",
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1095 "*19",
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1096 "*20",
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1097 "*26",
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1098 "*34",
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1099 "*36",
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bgruening
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1100 "*37",
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1101 "*38"
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bgruening
parents:
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1102 ],
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bgruening
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1103 "phased": false,
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1160 "*7",
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1161 "*13",
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1162 "*18",
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1163 "*19",
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1164 "*20",
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1165 "*26",
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1166 "*34",
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1167 "*36",
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1168 "*37",
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1169 "*38"
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1170 ],
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1181 "call": "G|G",
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1183 "*35"
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1184 ],
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1189 },
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1287 },
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bgruening
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1288 {
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1289 "gene": "CYP2B6",
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1290 "chromosome": "chr19",
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diff changeset
1292 "dbSnpId": "rs35010098",
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parents:
diff changeset
1293 "call": "C|C",
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1294 "alleles": [
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1295 "*21"
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1296 ],
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1297 "phased": false,
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1298 "wildtypeAllele": "C",
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1300 "warnings": []
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1301 },
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1302 {
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1303 "gene": "CYP2B6",
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1304 "chromosome": "chr19",
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1306 "dbSnpId": "rs3211369",
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1307 "call": "A|A",
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1308 "alleles": [
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1309 "*23"
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1310 ],
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1311 "phased": false,
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1312 "wildtypeAllele": "A",
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1314 "warnings": []
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1315 },
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1316 {
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1317 "gene": "CYP2B6",
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1318 "chromosome": "chr19",
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1320 "dbSnpId": "rs564083989",
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1321 "call": "G|G",
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bgruening
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1322 "alleles": [
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1323 "*24"
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bgruening
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1324 ],
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1325 "phased": false,
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1326 "wildtypeAllele": "G",
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1327 "mismatch": false,
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1328 "warnings": []
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bgruening
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1329 },
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bgruening
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1330 {
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1331 "gene": "CYP2B6",
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1332 "chromosome": "chr19",
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bgruening
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1333 "position": 41016805,
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bgruening
parents:
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1334 "dbSnpId": null,
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bgruening
parents:
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1335 "call": "A|A",
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bgruening
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1336 "alleles": [
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bgruening
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1337 "*25"
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bgruening
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1338 ],
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bgruening
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1339 "phased": false,
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1340 "wildtypeAllele": "A",
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1341 "mismatch": false,
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1342 "warnings": []
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bgruening
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1343 },
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bgruening
parents:
diff changeset
1344 {
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bgruening
parents:
diff changeset
1345 "gene": "CYP2B6",
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diff changeset
1346 "chromosome": "chr19",
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1347 "position": 41016810,
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bgruening
parents:
diff changeset
1348 "dbSnpId": "rs3211371",
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bgruening
parents:
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1349 "call": "C|C",
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bgruening
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1350 "alleles": [
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1351 "*5",
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bgruening
parents:
diff changeset
1352 "*7",
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bgruening
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1353 "*33",
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parents:
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1354 "*34"
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bgruening
parents:
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1355 ],
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bgruening
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1356 "phased": false,
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parents:
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1357 "wildtypeAllele": "C",
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bgruening
parents: 0
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1358 "mismatch": false,
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bgruening
parents: 0
diff changeset
1359 "warnings": []
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bgruening
parents:
diff changeset
1360 }
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bgruening
parents:
diff changeset
1361 ],
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bgruening
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diff changeset
1362 "variantsOfInterest": [],
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bgruening
parents:
diff changeset
1363 "highlightedVariants": []
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1364 },
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bgruening
parents:
diff changeset
1365 {
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parents:
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1366 "geneSymbol": "CYP2C19",
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bgruening
parents:
diff changeset
1367 "chr": "chr10",
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bgruening
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diff changeset
1368 "phased": true,
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bgruening
parents:
diff changeset
1369 "callSource": "MATCHER",
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bgruening
parents:
diff changeset
1370 "uncalledHaplotypes": [],
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bgruening
parents:
diff changeset
1371 "messages": [],
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bgruening
parents:
diff changeset
1372 "relatedDrugs": [],
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bgruening
parents:
diff changeset
1373 "matcherDiplotypes": [
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bgruening
parents:
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1374 {
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bgruening
parents:
diff changeset
1375 "allele1": {
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bgruening
parents:
diff changeset
1376 "gene": "CYP2C19",
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bgruening
parents:
diff changeset
1377 "name": "*38",
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bgruening
parents:
diff changeset
1378 "function": "Normal function",
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1379 "reference": true
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1380 },
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1381 "allele2": {
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1382 "gene": "CYP2C19",
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1383 "name": "*38",
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1384 "function": "Normal function",
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1385 "reference": true
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1386 },
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1387 "gene": "CYP2C19",
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1388 "phenotypes": [
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1389 "Normal Metabolizer"
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1390 ],
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1391 "variant": null,
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1392 "lookupKey": [
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1393 "Normal Metabolizer"
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1394 ],
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1395 "label": "*38/*38"
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1396 }
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1397 ],
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1398 "diplotypes": [
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1399 {
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1400 "allele1": {
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1401 "gene": "CYP2C19",
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1402 "name": "*38",
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1403 "function": "Normal function",
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1404 "reference": true
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1405 },
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1406 "allele2": {
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1407 "gene": "CYP2C19",
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1408 "name": "*38",
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1409 "function": "Normal function",
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1410 "reference": true
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bgruening
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1411 },
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1412 "gene": "CYP2C19",
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1413 "phenotypes": [
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1414 "Normal Metabolizer"
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1415 ],
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1416 "variant": null,
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1417 "lookupKey": [
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1418 "Normal Metabolizer"
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1419 ],
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1420 "label": "*38/*38"
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1421 }
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bgruening
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1422 ],
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1423 "variants": [
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1424 {
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1425 "gene": "CYP2C19",
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1426 "chromosome": "chr10",
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1427 "position": 94761900,
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1428 "dbSnpId": "rs12248560",
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bgruening
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1429 "call": "C|C",
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parents:
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1430 "alleles": [
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1431 "*4",
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1432 "*17"
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1433 ],
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1434 "phased": false,
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1435 "wildtypeAllele": "C",
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1436 "mismatch": false,
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1437 "warnings": []
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1438 },
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bgruening
parents:
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1439 {
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1440 "gene": "CYP2C19",
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1441 "chromosome": "chr10",
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1442 "position": 94762706,
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1443 "dbSnpId": "rs28399504",
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1444 "call": "A|A",
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bgruening
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1445 "alleles": [
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diff changeset
1446 "*4"
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bgruening
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1447 ],
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bgruening
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1448 "phased": false,
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1449 "wildtypeAllele": "A",
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1450 "mismatch": false,
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1451 "warnings": []
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bgruening
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1452 },
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bgruening
parents:
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1453 {
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parents:
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1454 "gene": "CYP2C19",
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1455 "chromosome": "chr10",
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parents:
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1456 "position": 94762712,
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bgruening
parents:
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1457 "dbSnpId": "rs367543002",
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parents:
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1458 "call": "C|C",
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bgruening
parents:
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1459 "alleles": [
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bgruening
parents:
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1460 "*34"
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bgruening
parents:
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1461 ],
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bgruening
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1462 "phased": false,
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1463 "wildtypeAllele": "C",
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1464 "mismatch": false,
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bgruening
parents: 0
diff changeset
1465 "warnings": []
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bgruening
parents:
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1466 },
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bgruening
parents:
diff changeset
1467 {
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parents:
diff changeset
1468 "gene": "CYP2C19",
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bgruening
parents:
diff changeset
1469 "chromosome": "chr10",
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bgruening
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1505 "*39"
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1519 "*29"
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1520 ],
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1533 "*19"
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1534 ],
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1539 },
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1547 "*30"
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1548 ],
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1553 },
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1559 "call": "C|C",
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1560 "alleles": [
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1561 "*31"
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1646 "*6"
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1751 },
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1765 },
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1773 "*7"
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1774 ],
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1779 },
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1787 "*18"
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1788 ],
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1789 "phased": false,
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1793 },
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bgruening
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1794 {
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1795 "gene": "CYP2C19",
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1796 "chromosome": "chr10",
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1798 "dbSnpId": "rs3758581",
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1799 "call": "A|A",
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parents:
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1800 "alleles": [
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1801 "*2",
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1802 "*3",
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1803 "*4",
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1804 "*5",
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1805 "*6",
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1806 "*8",
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1807 "*9",
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1808 "*10",
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1809 "*11",
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bgruening
parents:
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1810 "*12",
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bgruening
parents:
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1811 "*13",
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bgruening
parents:
diff changeset
1812 "*14",
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bgruening
parents:
diff changeset
1813 "*15",
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bgruening
parents:
diff changeset
1814 "*17",
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bgruening
parents:
diff changeset
1815 "*18",
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bgruening
parents:
diff changeset
1816 "*19",
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bgruening
parents:
diff changeset
1817 "*22",
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bgruening
parents:
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1818 "*23",
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bgruening
parents:
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1819 "*24",
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bgruening
parents:
diff changeset
1820 "*25",
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bgruening
parents:
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1821 "*26",
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bgruening
parents:
diff changeset
1822 "*28",
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bgruening
parents:
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1823 "*29",
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bgruening
parents:
diff changeset
1824 "*31",
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bgruening
parents:
diff changeset
1825 "*32",
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bgruening
parents:
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1826 "*33",
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bgruening
parents:
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1827 "*35",
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bgruening
parents:
diff changeset
1828 "*39"
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bgruening
parents:
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1829 ],
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bgruening
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1830 "phased": false,
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bgruening
parents:
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1831 "wildtypeAllele": "A",
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1832 "mismatch": false,
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diff changeset
1833 "warnings": []
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bgruening
parents:
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1834 },
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bgruening
parents:
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1835 {
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1871 ],
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1884 "*5"
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1885 ],
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1898 "*16"
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1899 ],
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1904 },
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1911 "alleles": [
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1912 "*25"
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1913 ],
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1914 "phased": false,
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1918 },
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1921 "chromosome": "chr10",
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1923 "dbSnpId": "rs55640102",
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1924 "call": "A|A",
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1925 "alleles": [
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diff changeset
1926 "*12"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1927 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1928 "phased": false,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1929 "wildtypeAllele": "A",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1930 "mismatch": false,
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1931 "warnings": []
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1932 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1933 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1934 "variantsOfInterest": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1935 "highlightedVariants": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1936 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1937 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1938 "geneSymbol": "CYP2C9",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1939 "chr": "chr10",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1940 "phased": true,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1941 "callSource": "MATCHER",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1942 "uncalledHaplotypes": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1943 "*72",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1944 "*73",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1945 "*74",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1946 "*75",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1947 "*76",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1948 "*77",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1949 "*78",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1950 "*79",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1951 "*80",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1952 "*81",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1953 "*82",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1954 "*83",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1955 "*84",
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1956 "*85"
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1957 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1958 "messages": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1959 "relatedDrugs": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1960 "matcherDiplotypes": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1961 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1962 "allele1": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1963 "gene": "CYP2C9",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1964 "name": "*1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1965 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1966 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1967 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1968 "allele2": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1969 "gene": "CYP2C9",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1970 "name": "*1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1971 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1972 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1973 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1974 "gene": "CYP2C9",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1975 "phenotypes": [
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1976 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1977 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1978 "variant": null,
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1979 "lookupKey": [
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1980 "2"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
1981 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1982 "label": "*1/*1"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1983 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1984 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1985 "diplotypes": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1986 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1987 "allele1": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1988 "gene": "CYP2C9",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1989 "name": "*1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1990 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1991 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1992 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1993 "allele2": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1994 "gene": "CYP2C9",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1995 "name": "*1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1996 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1997 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1998 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
1999 "gene": "CYP2C9",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
2000 "phenotypes": [
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
2001 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
2002 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2003 "variant": null,
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
2004 "lookupKey": [
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
2005 "2"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
2006 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2007 "label": "*1/*1"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2008 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2009 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2010 "variants": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2011 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2012 "gene": "CYP2C9",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2013 "chromosome": "chr10",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2014 "position": 94938683,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2015 "dbSnpId": "rs114071557",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2016 "call": "A|A",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2017 "alleles": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2018 "*36"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
2019 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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3113 "gene": "CYP2C9",
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bgruening
parents:
diff changeset
3114 "chromosome": "chr10",
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bgruening
parents:
diff changeset
3115 "position": 94986136,
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bgruening
parents:
diff changeset
3116 "dbSnpId": "rs1254213342",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3117 "call": null,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3118 "alleles": [
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bgruening
parents:
diff changeset
3119 "*75"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3120 ],
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bgruening
parents:
diff changeset
3121 "phased": false,
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bgruening
parents:
diff changeset
3122 "wildtypeAllele": "A",
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bgruening
parents: 0
diff changeset
3123 "mismatch": false,
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bgruening
parents: 0
diff changeset
3124 "warnings": []
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bgruening
parents: 0
diff changeset
3125 },
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bgruening
parents: 0
diff changeset
3126 {
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bgruening
parents: 0
diff changeset
3127 "gene": "CYP2C9",
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bgruening
parents: 0
diff changeset
3128 "chromosome": "chr10",
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bgruening
parents: 0
diff changeset
3129 "position": 94986174,
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bgruening
parents: 0
diff changeset
3130 "dbSnpId": "rs1441296358",
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bgruening
parents: 0
diff changeset
3131 "call": null,
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bgruening
parents: 0
diff changeset
3132 "alleles": [
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bgruening
parents: 0
diff changeset
3133 "*84"
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bgruening
parents: 0
diff changeset
3134 ],
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bgruening
parents: 0
diff changeset
3135 "phased": false,
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bgruening
parents: 0
diff changeset
3136 "wildtypeAllele": "G",
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bgruening
parents: 0
diff changeset
3137 "mismatch": false,
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bgruening
parents: 0
diff changeset
3138 "warnings": []
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3139 }
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bgruening
parents:
diff changeset
3140 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3141 "variantsOfInterest": [
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bgruening
parents:
diff changeset
3142 {
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bgruening
parents:
diff changeset
3143 "gene": "CYP2C9",
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bgruening
parents:
diff changeset
3144 "chromosome": "chr10",
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bgruening
parents:
diff changeset
3145 "position": 94645745,
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bgruening
parents:
diff changeset
3146 "dbSnpId": "rs12777823",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3147 "call": "G|G",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3148 "alleles": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3149 "phased": false,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3150 "wildtypeAllele": null,
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3151 "mismatch": false,
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3152 "warnings": []
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3153 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3154 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3155 "highlightedVariants": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3156 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3157 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3158 "geneSymbol": "CYP3A5",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3159 "chr": "chr7",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3160 "phased": true,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3161 "callSource": "MATCHER",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3162 "uncalledHaplotypes": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3163 "messages": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3164 {
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bgruening
parents:
diff changeset
3165 "rule_name": "CYP3A5 reverse complement footnote",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3166 "version": "1",
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bgruening
parents:
diff changeset
3167 "matches": {
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bgruening
parents:
diff changeset
3168 "gene": "CYP3A5",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3169 "hapsCalled": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3170 "hapsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3171 "variantsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3172 "variant": "",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3173 "dips": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3174 "drugs": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3175 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3176 "exception_type": "footnote",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3177 "message": "The CYP3A5 gene is on the negative chromosomal strand, all genotype calls for CYP3A5 in this report refer to the positive chromosomal strand. Therefore, genotype calls are complemented from gene bases."
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3178 }
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bgruening
parents:
diff changeset
3179 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3180 "relatedDrugs": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3181 "matcherDiplotypes": [
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bgruening
parents:
diff changeset
3182 {
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bgruening
parents:
diff changeset
3183 "allele1": {
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bgruening
parents:
diff changeset
3184 "gene": "CYP3A5",
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bgruening
parents:
diff changeset
3185 "name": "*1",
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bgruening
parents:
diff changeset
3186 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3187 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3188 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3189 "allele2": {
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bgruening
parents:
diff changeset
3190 "gene": "CYP3A5",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3191 "name": "*1",
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bgruening
parents:
diff changeset
3192 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3193 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3194 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3195 "gene": "CYP3A5",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3196 "phenotypes": [
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3197 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3198 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3199 "variant": null,
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3200 "lookupKey": [
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3201 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3202 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3203 "label": "*1/*1"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3204 }
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3384 }
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diff changeset
3387 "highlightedVariants": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3388 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3389 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3390 "geneSymbol": "DPYD",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3391 "chr": "chr1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3392 "phased": true,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3393 "callSource": "MATCHER",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3394 "uncalledHaplotypes": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3395 "messages": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3396 {
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bgruening
parents:
diff changeset
3397 "rule_name": "DPYD reverse complement footnote",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3398 "version": "1",
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bgruening
parents:
diff changeset
3399 "matches": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3400 "gene": "DPYD",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3401 "hapsCalled": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3402 "hapsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3403 "variantsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3404 "variant": "",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3405 "dips": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3406 "drugs": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3407 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3408 "exception_type": "footnote",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3409 "message": "The DPYD gene is on the negative chromosomal strand, all genotype calls for DPYD in this report refer to the positive chromosomal strand. Therefore, genotype calls are complemented from gene bases."
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3410 }
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bgruening
parents:
diff changeset
3411 ],
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bgruening
parents:
diff changeset
3412 "relatedDrugs": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3413 "matcherDiplotypes": [
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bgruening
parents:
diff changeset
3414 {
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bgruening
parents:
diff changeset
3415 "allele1": {
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bgruening
parents:
diff changeset
3416 "gene": "DPYD",
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bgruening
parents:
diff changeset
3417 "name": "Reference",
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bgruening
parents:
diff changeset
3418 "function": "Normal function",
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bgruening
parents:
diff changeset
3419 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3420 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3421 "allele2": {
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bgruening
parents:
diff changeset
3422 "gene": "DPYD",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3423 "name": "Reference",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3424 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3425 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3426 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3427 "gene": "DPYD",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3428 "phenotypes": [
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bgruening
parents: 0
diff changeset
3429 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3430 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3431 "variant": null,
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3432 "lookupKey": [
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bgruening
parents: 0
diff changeset
3433 "2"
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bgruening
parents: 0
diff changeset
3434 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3435 "label": "Reference/Reference"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3436 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3437 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3438 "diplotypes": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3439 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3440 "allele1": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3441 "gene": "DPYD",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3442 "name": "Reference",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3443 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3444 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3445 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3446 "allele2": {
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bgruening
parents:
diff changeset
3447 "gene": "DPYD",
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bgruening
parents:
diff changeset
3448 "name": "Reference",
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bgruening
parents:
diff changeset
3449 "function": "Normal function",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3450 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3451 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3452 "gene": "DPYD",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3453 "phenotypes": [
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bgruening
parents: 0
diff changeset
3454 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3455 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3456 "variant": null,
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3457 "lookupKey": [
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3458 "2"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3459 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3460 "label": "Reference/Reference"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3461 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3462 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3463 "variants": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3464 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3465 "gene": "DPYD",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3466 "chromosome": "chr1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3467 "position": 97078987,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3468 "dbSnpId": "rs114096998",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3469 "call": "G|G",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3470 "alleles": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3471 "c.3067C\u003eA"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3472 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3473 "phased": false,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3474 "wildtypeAllele": "G",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3475 "mismatch": false,
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
3476 "warnings": []
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3477 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3478 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
3479 "gene": "DPYD",
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4565 "phased": false,
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4566 "wildtypeAllele": "GATGA",
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4575 "call": "A|A",
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4577 "c.85T\u003eC (*9A)"
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4586 "chromosome": "chr1",
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4589 "call": "C|C",
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4591 "c.62G\u003eA"
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4592 ],
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4593 "phased": false,
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4597 },
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4600 "chromosome": "chr1",
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4603 "call": "G|G",
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4604 "alleles": [
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bgruening
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4605 "c.61C\u003eT"
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4606 ],
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bgruening
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4607 "phased": false,
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4608 "wildtypeAllele": "G",
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4609 "mismatch": false,
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4610 "warnings": []
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4611 },
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4612 {
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4613 "gene": "DPYD",
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4614 "chromosome": "chr1",
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4615 "position": 97883368,
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bgruening
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4616 "dbSnpId": "rs150036960",
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bgruening
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4617 "call": "G|G",
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bgruening
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4618 "alleles": [
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bgruening
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4619 "c.46C\u003eG"
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bgruening
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4620 ],
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bgruening
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4621 "phased": false,
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4622 "wildtypeAllele": "G",
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4623 "mismatch": false,
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4624 "warnings": []
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bgruening
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4625 }
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bgruening
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4626 ],
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bgruening
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diff changeset
4627 "variantsOfInterest": [],
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bgruening
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diff changeset
4628 "highlightedVariants": []
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bgruening
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4629 },
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bgruening
parents:
diff changeset
4630 {
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bgruening
parents:
diff changeset
4631 "geneSymbol": "IFNL3",
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bgruening
parents:
diff changeset
4632 "chr": "chr19",
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bgruening
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diff changeset
4633 "phased": true,
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bgruening
parents:
diff changeset
4634 "callSource": "MATCHER",
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bgruening
parents:
diff changeset
4635 "uncalledHaplotypes": [],
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bgruening
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4636 "messages": [
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bgruening
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diff changeset
4637 {
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bgruening
parents:
diff changeset
4638 "rule_name": "IFNL3 reverse complement footnote",
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bgruening
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diff changeset
4639 "version": "1",
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bgruening
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diff changeset
4640 "matches": {
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bgruening
parents:
diff changeset
4641 "gene": "IFNL3",
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bgruening
parents:
diff changeset
4642 "hapsCalled": [],
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bgruening
parents:
diff changeset
4643 "hapsMissing": [],
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bgruening
parents:
diff changeset
4644 "variantsMissing": [],
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bgruening
parents:
diff changeset
4645 "variant": "",
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bgruening
parents:
diff changeset
4646 "dips": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
4647 "drugs": []
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bgruening
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diff changeset
4648 },
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bgruening
parents:
diff changeset
4649 "exception_type": "footnote",
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bgruening
parents:
diff changeset
4650 "message": "The IFNL3 gene is on the negative chromosomal strand, all genotype calls for IFNL3 in this report refer to the positive chromosomal strand. Therefore, genotype calls are complemented from gene bases."
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bgruening
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diff changeset
4651 }
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bgruening
parents:
diff changeset
4652 ],
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bgruening
parents:
diff changeset
4653 "relatedDrugs": [],
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bgruening
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4825 "*5"
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5816 "*13"
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5831 "*15",
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5832 "*20",
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5833 "*24",
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5834 "*25",
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5835 "*27",
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5836 "*28",
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5837 "*29",
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bgruening
parents:
diff changeset
6204 "call": null,
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bgruening
parents:
diff changeset
6205 "alleles": [
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bgruening
parents:
diff changeset
6206 "*47"
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bgruening
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diff changeset
6207 ],
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bgruening
parents:
diff changeset
6208 "phased": false,
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diff changeset
6209 "wildtypeAllele": "C",
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6210 "mismatch": false,
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6211 "warnings": []
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diff changeset
6212 },
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bgruening
parents:
diff changeset
6213 {
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6214 "gene": "SLCO1B1",
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diff changeset
6215 "chromosome": "chr12",
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6216 "position": 21206031,
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6217 "dbSnpId": "rs74064213",
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bgruening
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6218 "call": null,
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bgruening
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6219 "alleles": [
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bgruening
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6220 "*43",
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bgruening
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diff changeset
6221 "*44"
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bgruening
parents:
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6222 ],
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bgruening
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6223 "phased": false,
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bgruening
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6224 "wildtypeAllele": "A",
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bgruening
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6225 "mismatch": false,
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bgruening
parents: 0
diff changeset
6226 "warnings": []
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bgruening
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diff changeset
6227 },
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bgruening
parents:
diff changeset
6228 {
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parents:
diff changeset
6229 "gene": "SLCO1B1",
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bgruening
parents:
diff changeset
6230 "chromosome": "chr12",
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bgruening
parents:
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6231 "position": 21222355,
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bgruening
parents:
diff changeset
6232 "dbSnpId": "rs71581941",
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bgruening
parents:
diff changeset
6233 "call": null,
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bgruening
parents:
diff changeset
6234 "alleles": [
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bgruening
parents:
diff changeset
6235 "*45",
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bgruening
parents:
diff changeset
6236 "*46"
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bgruening
parents:
diff changeset
6237 ],
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bgruening
parents:
diff changeset
6238 "phased": false,
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bgruening
parents:
diff changeset
6239 "wildtypeAllele": "C",
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bgruening
parents: 0
diff changeset
6240 "mismatch": false,
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bgruening
parents: 0
diff changeset
6241 "warnings": []
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bgruening
parents:
diff changeset
6242 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
6243 ],
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bgruening
parents:
diff changeset
6244 "variantsOfInterest": [],
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bgruening
parents:
diff changeset
6245 "highlightedVariants": [
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bgruening
parents:
diff changeset
6246 "rs4149056T/rs4149056T"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
6247 ]
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
6248 },
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bgruening
parents:
diff changeset
6249 {
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bgruening
parents:
diff changeset
6250 "geneSymbol": "TPMT",
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bgruening
parents:
diff changeset
6251 "chr": "chr6",
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bgruening
parents:
diff changeset
6252 "phased": true,
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bgruening
parents:
diff changeset
6253 "callSource": "MATCHER",
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bgruening
parents:
diff changeset
6254 "uncalledHaplotypes": [],
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bgruening
parents:
diff changeset
6255 "messages": [
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bgruening
parents:
diff changeset
6256 {
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bgruening
parents:
diff changeset
6257 "rule_name": "TPMT reverse complement footnote",
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bgruening
parents:
diff changeset
6258 "version": "1",
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bgruening
parents:
diff changeset
6259 "matches": {
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bgruening
parents:
diff changeset
6260 "gene": "TPMT",
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bgruening
parents:
diff changeset
6261 "hapsCalled": [],
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bgruening
parents:
diff changeset
6262 "hapsMissing": [],
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bgruening
parents:
diff changeset
6263 "variantsMissing": [],
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bgruening
parents:
diff changeset
6264 "variant": "",
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bgruening
parents:
diff changeset
6265 "dips": [],
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bgruening
parents:
diff changeset
6266 "drugs": []
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bgruening
parents:
diff changeset
6267 },
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bgruening
parents:
diff changeset
6268 "exception_type": "footnote",
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bgruening
parents:
diff changeset
6269 "message": "The TPMT gene is on the negative chromosomal strand, all genotype calls for TPMT in this report refer to the positive chromosomal strand. Therefore, genotype calls are complemented from gene bases."
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
6270 }
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bgruening
parents:
diff changeset
6271 ],
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bgruening
parents:
diff changeset
6272 "relatedDrugs": [],
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bgruening
parents:
diff changeset
6273 "matcherDiplotypes": [
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bgruening
parents:
diff changeset
6274 {
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bgruening
parents:
diff changeset
6275 "allele1": {
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bgruening
parents:
diff changeset
6276 "gene": "TPMT",
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bgruening
parents:
diff changeset
6277 "name": "*1",
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bgruening
parents:
diff changeset
6278 "function": "Normal Function",
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bgruening
parents:
diff changeset
6279 "reference": true
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bgruening
parents:
diff changeset
6280 },
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bgruening
parents:
diff changeset
6281 "allele2": {
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bgruening
parents:
diff changeset
6282 "gene": "TPMT",
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bgruening
parents:
diff changeset
6283 "name": "*1",
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bgruening
parents:
diff changeset
6284 "function": "Normal Function",
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bgruening
parents:
diff changeset
6285 "reference": true
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
6286 },
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bgruening
parents:
diff changeset
6287 "gene": "TPMT",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
6288 "phenotypes": [
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bgruening
parents: 0
diff changeset
6289 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
6290 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
6291 "variant": null,
1
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bgruening
parents: 0
diff changeset
6292 "lookupKey": [
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bgruening
parents: 0
diff changeset
6293 "Normal Metabolizer"
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
6294 ],
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
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6933 },
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bgruening
parents:
diff changeset
6934 {
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parents:
diff changeset
6935 "geneSymbol": "UGT1A1",
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parents:
diff changeset
6936 "chr": "chr2",
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parents:
diff changeset
6937 "phased": true,
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parents:
diff changeset
6938 "callSource": "MATCHER",
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parents:
diff changeset
6939 "uncalledHaplotypes": [],
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parents:
diff changeset
6940 "messages": [
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diff changeset
6941 {
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diff changeset
6942 "rule_name": "UGT1A1 repeat warning",
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diff changeset
6943 "version": "1",
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diff changeset
6944 "matches": {
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parents:
diff changeset
6945 "gene": "UGT1A1",
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parents:
diff changeset
6946 "hapsCalled": [],
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diff changeset
6947 "hapsMissing": [],
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diff changeset
6948 "variantsMissing": [],
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diff changeset
6949 "variant": "",
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diff changeset
6950 "dips": [],
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diff changeset
6951 "drugs": []
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diff changeset
6952 },
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diff changeset
6953 "exception_type": "footnote",
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diff changeset
6954 "message": "Some alleles in UGT1A1 are distinguished by a repeat sequence; some genotyping technologies may not accurately call the repeat."
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diff changeset
6955 }
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diff changeset
6956 ],
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6957 "relatedDrugs": [],
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6958 "matcherDiplotypes": [
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diff changeset
6959 {
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diff changeset
6960 "allele1": {
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6961 "gene": "UGT1A1",
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6962 "name": "*1",
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6963 "function": "Normal function",
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diff changeset
6964 "reference": true
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diff changeset
6965 },
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diff changeset
6966 "allele2": {
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6967 "gene": "UGT1A1",
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diff changeset
6968 "name": "*1",
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diff changeset
6969 "function": "Normal function",
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diff changeset
6970 "reference": true
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bgruening
parents:
diff changeset
6971 },
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6972 "gene": "UGT1A1",
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diff changeset
6973 "phenotypes": [
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bgruening
parents: 0
diff changeset
6974 "Normal Metabolizer"
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diff changeset
6975 ],
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6976 "variant": null,
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diff changeset
6977 "lookupKey": [
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diff changeset
6978 "Normal Metabolizer"
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6979 ],
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6980 "label": "*1/*1"
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6981 }
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6982 ],
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6983 "diplotypes": [
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6984 {
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diff changeset
6985 "allele1": {
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6986 "gene": "UGT1A1",
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6987 "name": "*1",
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6988 "function": "Normal function",
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6989 "reference": true
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6990 },
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6991 "allele2": {
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parents:
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6992 "gene": "UGT1A1",
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6993 "name": "*1",
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bgruening
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diff changeset
6994 "function": "Normal function",
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bgruening
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6995 "reference": true
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bgruening
parents:
diff changeset
6996 },
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bgruening
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diff changeset
6997 "gene": "UGT1A1",
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bgruening
parents: 0
diff changeset
6998 "phenotypes": [
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bgruening
parents: 0
diff changeset
6999 "Normal Metabolizer"
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diff changeset
7000 ],
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7001 "variant": null,
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parents: 0
diff changeset
7002 "lookupKey": [
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bgruening
parents: 0
diff changeset
7003 "Normal Metabolizer"
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7004 ],
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7005 "label": "*1/*1"
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parents:
diff changeset
7006 }
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7007 ],
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7008 "variants": [
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bgruening
parents:
diff changeset
7009 {
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7010 "gene": "UGT1A1",
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7011 "chromosome": "chr2",
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7012 "position": 233759924,
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parents:
diff changeset
7013 "dbSnpId": "rs887829",
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bgruening
parents:
diff changeset
7014 "call": "C|C",
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bgruening
parents:
diff changeset
7015 "alleles": [
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parents:
diff changeset
7016 "*80",
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bgruening
parents:
diff changeset
7017 "*80+*28",
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bgruening
parents:
diff changeset
7018 "*80+*37"
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bgruening
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7019 ],
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bgruening
parents:
diff changeset
7020 "phased": false,
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bgruening
parents:
diff changeset
7021 "wildtypeAllele": "C",
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bgruening
parents: 0
diff changeset
7022 "mismatch": false,
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bgruening
parents: 0
diff changeset
7023 "warnings": []
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bgruening
parents:
diff changeset
7024 },
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bgruening
parents:
diff changeset
7025 {
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bgruening
parents:
diff changeset
7026 "gene": "UGT1A1",
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bgruening
parents:
diff changeset
7027 "chromosome": "chr2",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7028 "position": 233760233,
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bgruening
parents:
diff changeset
7029 "dbSnpId": "rs3064744",
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bgruening
parents:
diff changeset
7030 "call": "CAT|CAT",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7031 "alleles": [
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bgruening
parents:
diff changeset
7032 "*28",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7033 "*36",
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bgruening
parents:
diff changeset
7034 "*37",
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bgruening
parents:
diff changeset
7035 "*80+*28",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7036 "*80+*37"
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bgruening
parents:
diff changeset
7037 ],
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bgruening
parents:
diff changeset
7038 "phased": false,
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bgruening
parents:
diff changeset
7039 "wildtypeAllele": "CAT",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
7040 "mismatch": false,
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bgruening
parents: 0
diff changeset
7041 "warnings": []
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7042 },
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bgruening
parents:
diff changeset
7043 {
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bgruening
parents:
diff changeset
7044 "gene": "UGT1A1",
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bgruening
parents:
diff changeset
7045 "chromosome": "chr2",
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bgruening
parents:
diff changeset
7046 "position": 233760498,
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bgruening
parents:
diff changeset
7047 "dbSnpId": "rs4148323",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7048 "call": "G|G",
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bgruening
parents:
diff changeset
7049 "alleles": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7050 "*6"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7051 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7052 "phased": false,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7053 "wildtypeAllele": "G",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
7054 "mismatch": false,
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bgruening
parents: 0
diff changeset
7055 "warnings": []
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7056 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7057 {
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bgruening
parents:
diff changeset
7058 "gene": "UGT1A1",
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bgruening
parents:
diff changeset
7059 "chromosome": "chr2",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7060 "position": 233760973,
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bgruening
parents:
diff changeset
7061 "dbSnpId": "rs35350960",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7062 "call": "C|C",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7063 "alleles": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7064 "*27"
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7065 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7066 "phased": false,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7067 "wildtypeAllele": "C",
1
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
7068 "mismatch": false,
891283e0ee89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
bgruening
parents: 0
diff changeset
7069 "warnings": []
0
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7070 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7071 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7072 "variantsOfInterest": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7073 "highlightedVariants": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7074 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7075 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7076 "geneSymbol": "VKORC1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7077 "chr": "chr16",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7078 "phased": true,
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7079 "callSource": "MATCHER",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7080 "uncalledHaplotypes": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7081 "messages": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7082 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7083 "rule_name": "VKORC1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7084 "version": "1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7085 "matches": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7086 "gene": "VKORC1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7087 "hapsCalled": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7088 "hapsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7089 "variantsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7090 "variant": "",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7091 "dips": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7092 "drugs": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7093 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7094 "exception_type": "footnote",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7095 "message": "CPIC recommendations for warfarin use only rs9923231; however, other variants in VKORC1 may have functional consequences and may be more common in some populations."
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7096 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7097 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7098 "rule_name": "VKORC1 reverse complement footnote",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7099 "version": "1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7100 "matches": {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7101 "gene": "VKORC1",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7102 "hapsCalled": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7103 "hapsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7104 "variantsMissing": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7105 "variant": "",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7106 "dips": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7107 "drugs": []
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7108 },
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7109 "exception_type": "footnote",
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7110 "message": "The VKORC1 gene is on the negative chromosomal strand, all genotype calls for VKORC1 in this report refer to the positive chromosomal strand. Therefore, genotype calls are complemented from gene bases."
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7111 }
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7112 ],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7113 "relatedDrugs": [],
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7114 "matcherDiplotypes": [
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7115 {
d67642a21a1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
bgruening
parents:
diff changeset
7116 "allele1": {
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7133 }
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bgruening
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7154 }
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7155 ],
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7156 "variants": [
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7157 {
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7162 "call": "C|C",
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7163 "alleles": [
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7164 "rs9923231 variant (T)"
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7165 ],
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7166 "phased": false,
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7169 "warnings": []
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7170 }
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7171 ],
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7173 "highlightedVariants": []
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7174 }
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bgruening
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7175 ]