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comparison test-data/test_2.json @ 1:8005ce1418ac draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
author bgruening
date Thu, 05 May 2022 20:26:42 +0000
parents 28aa54c800c0
children
comparison
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0:28aa54c800c0 1:8005ce1418ac
1 { 1 {
2 "metadata": { 2 "metadata": {
3 "namedAlleleMatcherVersion": "1.0.0", 3 "namedAlleleMatcherVersion": "1.0.0",
4 "genomeBuild": "GRCh38.p13", 4 "genomeBuild": "GRCh38.p13",
5 "inputFilename": "input.vcf", 5 "inputFilename": "input.vcf",
6 "timestamp": "Jan 27, 2022, 11:53:07 PM" 6 "timestamp": "May 4, 2022, 8:57:03 PM"
7 }, 7 },
8 "results": [ 8 "results": [
9 { 9 {
10 "alleleDefinitionVersion": "01/10/22", 10 "alleleDefinitionVersion": "04/20/22",
11 "chromosome": "chr4",
12 "gene": "ABCG2",
13 "diplotypes": [],
14 "haplotypes": [],
15 "phased": true,
16 "variants": [],
17 "variantsOfInterest": [],
18 "matchData": {
19 "missingPositions": [
20 {
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22 "position": 88131171,
23 "cpicPosition": 88131171,
24 "rsid": "rs2231142",
25 "chromosomeHgvsName": "g.88131171G\u003eT",
26 "cpicAlleles": [
27 "G",
28 "T"
29 ],
30 "cpicToVcfAlleleMap": {
31 "T": "T",
32 "G": "G"
33 },
34 "ref": "G",
35 "alts": [
36 "T"
37 ]
38 }
39 ],
40 "mismatchedAlleles": []
41 },
42 "uncallableHaplotypes": [
43 "rs2231142 variant (T)",
44 "rs2231142 reference (G)"
45 ],
46 "ignoredHaplotypes": []
47 },
48 {
49 "alleleDefinitionVersion": "04/20/22",
11 "chromosome": "chr1", 50 "chromosome": "chr1",
12 "gene": "CACNA1S", 51 "gene": "CACNA1S",
13 "diplotypes": [ 52 "diplotypes": [
14 { 53 {
15 "name": "Reference/Reference", 54 "name": "Reference/Reference",
56 }, 95 },
57 "uncallableHaplotypes": [], 96 "uncallableHaplotypes": [],
58 "ignoredHaplotypes": [] 97 "ignoredHaplotypes": []
59 }, 98 },
60 { 99 {
61 "alleleDefinitionVersion": "01/10/22", 100 "alleleDefinitionVersion": "04/20/22",
62 "chromosome": "chr7", 101 "chromosome": "chr7",
63 "gene": "CFTR", 102 "gene": "CFTR",
64 "diplotypes": [ 103 "diplotypes": [
65 { 104 {
66 "name": "ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence", 105 "name": "ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence",
292 }, 331 },
293 "uncallableHaplotypes": [], 332 "uncallableHaplotypes": [],
294 "ignoredHaplotypes": [] 333 "ignoredHaplotypes": []
295 }, 334 },
296 { 335 {
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299 "gene": "CYP2B6", 338 "gene": "CYP2B6",
300 "diplotypes": [ 339 "diplotypes": [
301 { 340 {
302 "name": "*1/*1", 341 "name": "*1/*1",
508 }, 547 },
509 "uncallableHaplotypes": [], 548 "uncallableHaplotypes": [],
510 "ignoredHaplotypes": [] 549 "ignoredHaplotypes": []
511 }, 550 },
512 { 551 {
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515 "gene": "CYP2C19", 554 "gene": "CYP2C19",
516 "diplotypes": [ 555 "diplotypes": [
517 { 556 {
518 "name": "*38/*38", 557 "name": "*38/*38",
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720 "uncallableHaplotypes": [], 759 "uncallableHaplotypes": [],
721 "ignoredHaplotypes": [] 760 "ignoredHaplotypes": []
722 }, 761 },
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726 "gene": "CYP2C9", 765 "gene": "CYP2C9",
727 "diplotypes": [ 766 "diplotypes": [
728 { 767 {
729 "name": "*1/*1", 768 "name": "*1/*1",
1090 "vcfCall": "G|G" 1129 "vcfCall": "G|G"
1091 } 1130 }
1092 ], 1131 ],
1093 "matchData": { 1132 "matchData": {
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1170 ]
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1177 "chromosomeHgvsName": "g.94938800G\u003eA",
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1190 },
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1195 "rsid": null,
1196 "chromosomeHgvsName": "g.94941975G\u003eA",
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1199 "G"
1200 ],
1201 "cpicToVcfAlleleMap": {
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1208 ]
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1218 "T"
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1220 "cpicToVcfAlleleMap": {
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1227 ]
1228 },
1095 { 1229 {
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1097 "position": 94942306, 1231 "position": 94942306,
1098 "cpicPosition": 94942306, 1232 "cpicPosition": 94942306,
1099 "rsid": "rs1289704600", 1233 "rsid": "rs1289704600",
1149 "T" 1283 "T"
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1151 }, 1285 },
1152 { 1286 {
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1291 "chromosomeHgvsName": "g.94949145C\u003eT",
1292 "cpicAlleles": [
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1295 ],
1296 "cpicToVcfAlleleMap": {
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1298 "T": "T"
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1300 "ref": "C",
1301 "alts": [
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1303 ]
1304 },
1305 {
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1308 "cpicPosition": 94949163,
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1310 "chromosomeHgvsName": "g.94949163del",
1311 "cpicAlleles": [
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1313 "delT"
1314 ],
1315 "cpicToVcfAlleleMap": {
1316 "T": "AT",
1317 "delT": "A"
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1319 "ref": "AT",
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1322 ]
1323 },
1324 {
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1327 "cpicPosition": 94972183,
1328 "rsid": null,
1329 "chromosomeHgvsName": "g.94972183A\u003eT",
1330 "cpicAlleles": [
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1332 "T"
1333 ],
1334 "cpicToVcfAlleleMap": {
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1336 "T": "T"
1337 },
1338 "ref": "A",
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1341 ]
1342 },
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1346 "cpicPosition": 94981258,
1347 "rsid": "rs1297714792",
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1349 "cpicAlleles": [
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1351 "T"
1352 ],
1353 "cpicToVcfAlleleMap": {
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1356 },
1357 "ref": "C",
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1360 ]
1361 },
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1158 "cpicAlleles": [ 1368 "cpicAlleles": [
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1168 "C" 1378 "C"
1169 ] 1379 ]
1380 },
1381 {
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1384 "cpicPosition": 94986174,
1385 "rsid": "rs1441296358",
1386 "chromosomeHgvsName": "g.94986174G\u003eC",
1387 "cpicAlleles": [
1388 "C",
1389 "G"
1390 ],
1391 "cpicToVcfAlleleMap": {
1392 "C": "C",
1393 "G": "G"
1394 },
1395 "ref": "G",
1396 "alts": [
1397 "C"
1398 ]
1170 } 1399 }
1171 ], 1400 ],
1172 "mismatchedAlleles": [] 1401 "mismatchedAlleles": []
1173 }, 1402 },
1174 "uncallableHaplotypes": [ 1403 "uncallableHaplotypes": [
1404 "*80",
1405 "*81",
1406 "*82",
1175 "*72", 1407 "*72",
1408 "*83",
1176 "*73", 1409 "*73",
1410 "*84",
1177 "*74", 1411 "*74",
1178 "*75" 1412 "*85",
1413 "*75",
1414 "*76",
1415 "*77",
1416 "*78",
1417 "*79"
1179 ], 1418 ],
1180 "ignoredHaplotypes": [] 1419 "ignoredHaplotypes": []
1181 }, 1420 },
1182 { 1421 {
1183 "alleleDefinitionVersion": "01/10/22", 1422 "alleleDefinitionVersion": "04/20/22",
1184 "chromosome": "chr7", 1423 "chromosome": "chr7",
1185 "gene": "CYP3A5", 1424 "gene": "CYP3A5",
1186 "diplotypes": [ 1425 "diplotypes": [
1187 { 1426 {
1188 "name": "*1/*1", 1427 "name": "*1/*1",
1189 "haplotype1": { 1428 "haplotype1": {
1190 "name": "*1", 1429 "name": "*1",
1191 "sequences": [ 1430 "sequences": [
1192 "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;" 1431 "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;"
1193 ] 1432 ]
1194 }, 1433 },
1195 "haplotype2": { 1434 "haplotype2": {
1196 "name": "*1", 1435 "name": "*1",
1197 "sequences": [ 1436 "sequences": [
1198 "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;" 1437 "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;"
1199 ] 1438 ]
1200 }, 1439 },
1201 "score": 16 1440 "score": 10
1202 } 1441 }
1203 ], 1442 ],
1204 "haplotypes": [ 1443 "haplotypes": [
1205 { 1444 {
1206 "name": "*1", 1445 "name": "*1",
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1209 ] 1448 ]
1210 } 1449 }
1211 ], 1450 ],
1212 "phased": true, 1451 "phased": true,
1213 "variants": [ 1452 "variants": [
1214 { 1453 {
1215 "position": 99652613,
1216 "rsid": "rs28365083",
1217 "vcfCall": "G|G"
1218 },
1219 {
1220 "position": 99652770, 1454 "position": 99652770,
1221 "rsid": "rs41303343", 1455 "rsid": "rs41303343",
1222 "vcfCall": "T|T" 1456 "vcfCall": "T|T"
1223 }, 1457 },
1224 { 1458 {
1228 }, 1462 },
1229 { 1463 {
1230 "position": 99665212, 1464 "position": 99665212,
1231 "rsid": "rs10264272", 1465 "rsid": "rs10264272",
1232 "vcfCall": "C|C" 1466 "vcfCall": "C|C"
1233 },
1234 {
1235 "position": 99665237,
1236 "rsid": "rs56411402",
1237 "vcfCall": "T|T"
1238 },
1239 {
1240 "position": 99666950,
1241 "rsid": "rs55965422",
1242 "vcfCall": "A|A"
1243 }, 1467 },
1244 { 1468 {
1245 "position": 99672916, 1469 "position": 99672916,
1246 "rsid": "rs776746", 1470 "rsid": "rs776746",
1247 "vcfCall": "T|T" 1471 "vcfCall": "T|T"
1259 }, 1483 },
1260 "uncallableHaplotypes": [], 1484 "uncallableHaplotypes": [],
1261 "ignoredHaplotypes": [] 1485 "ignoredHaplotypes": []
1262 }, 1486 },
1263 { 1487 {
1264 "alleleDefinitionVersion": "01/10/22", 1488 "alleleDefinitionVersion": "04/20/22",
1265 "chromosome": "chr19", 1489 "chromosome": "chr19",
1266 "gene": "CYP4F2", 1490 "gene": "CYP4F2",
1267 "diplotypes": [ 1491 "diplotypes": [
1268 { 1492 {
1269 "name": "*1/*1", 1493 "name": "*1/*1",
1310 }, 1534 },
1311 "uncallableHaplotypes": [], 1535 "uncallableHaplotypes": [],
1312 "ignoredHaplotypes": [] 1536 "ignoredHaplotypes": []
1313 }, 1537 },
1314 { 1538 {
1315 "alleleDefinitionVersion": "01/10/22", 1539 "alleleDefinitionVersion": "04/20/22",
1316 "chromosome": "chr1", 1540 "chromosome": "chr1",
1317 "gene": "DPYD", 1541 "gene": "DPYD",
1318 "diplotypes": [ 1542 "diplotypes": [
1319 { 1543 {
1320 "name": "Reference/Reference", 1544 "name": "Reference/Reference",
1766 }, 1990 },
1767 "uncallableHaplotypes": [], 1991 "uncallableHaplotypes": [],
1768 "ignoredHaplotypes": [] 1992 "ignoredHaplotypes": []
1769 }, 1993 },
1770 { 1994 {
1771 "alleleDefinitionVersion": "01/10/22", 1995 "alleleDefinitionVersion": "04/20/22",
1772 "chromosome": "chr19", 1996 "chromosome": "chr19",
1773 "gene": "IFNL3", 1997 "gene": "IFNL3",
1774 "diplotypes": [ 1998 "diplotypes": [
1775 { 1999 {
1776 "name": "rs12979860 reference (C)/rs12979860 reference (C)", 2000 "name": "rs12979860 reference (C)/rs12979860 reference (C)",
1812 }, 2036 },
1813 "uncallableHaplotypes": [], 2037 "uncallableHaplotypes": [],
1814 "ignoredHaplotypes": [] 2038 "ignoredHaplotypes": []
1815 }, 2039 },
1816 { 2040 {
1817 "alleleDefinitionVersion": "01/10/22", 2041 "alleleDefinitionVersion": "04/20/22",
1818 "chromosome": "chr13", 2042 "chromosome": "chr13",
1819 "gene": "NUDT15", 2043 "gene": "NUDT15",
1820 "diplotypes": [ 2044 "diplotypes": [
1821 { 2045 {
1822 "name": "*1/*1", 2046 "name": "*1/*1",
1938 }, 2162 },
1939 "uncallableHaplotypes": [], 2163 "uncallableHaplotypes": [],
1940 "ignoredHaplotypes": [] 2164 "ignoredHaplotypes": []
1941 }, 2165 },
1942 { 2166 {
1943 "alleleDefinitionVersion": "01/10/22", 2167 "alleleDefinitionVersion": "04/20/22",
1944 "chromosome": "chr19", 2168 "chromosome": "chr19",
1945 "gene": "RYR1", 2169 "gene": "RYR1",
1946 "diplotypes": [ 2170 "diplotypes": [
1947 { 2171 {
1948 "name": "Reference/Reference", 2172 "name": "Reference/Reference",
2199 }, 2423 },
2200 "uncallableHaplotypes": [], 2424 "uncallableHaplotypes": [],
2201 "ignoredHaplotypes": [] 2425 "ignoredHaplotypes": []
2202 }, 2426 },
2203 { 2427 {
2204 "alleleDefinitionVersion": "01/10/22", 2428 "alleleDefinitionVersion": "04/20/22",
2205 "chromosome": "chr12", 2429 "chromosome": "chr12",
2206 "gene": "SLCO1B1", 2430 "gene": "SLCO1B1",
2207 "diplotypes": [ 2431 "diplotypes": [
2208 { 2432 {
2209 "name": "*1/*1", 2433 "name": "*1/*1",
2498 "*38" 2722 "*38"
2499 ], 2723 ],
2500 "ignoredHaplotypes": [] 2724 "ignoredHaplotypes": []
2501 }, 2725 },
2502 { 2726 {
2503 "alleleDefinitionVersion": "01/10/22", 2727 "alleleDefinitionVersion": "04/20/22",
2504 "chromosome": "chr6", 2728 "chromosome": "chr6",
2505 "gene": "TPMT", 2729 "gene": "TPMT",
2506 "diplotypes": [ 2730 "diplotypes": [
2507 { 2731 {
2508 "name": "*1/*1", 2732 "name": "*1/*1",
2754 }, 2978 },
2755 "uncallableHaplotypes": [], 2979 "uncallableHaplotypes": [],
2756 "ignoredHaplotypes": [] 2980 "ignoredHaplotypes": []
2757 }, 2981 },
2758 { 2982 {
2759 "alleleDefinitionVersion": "01/10/22", 2983 "alleleDefinitionVersion": "04/20/22",
2760 "chromosome": "chr2", 2984 "chromosome": "chr2",
2761 "gene": "UGT1A1", 2985 "gene": "UGT1A1",
2762 "diplotypes": [ 2986 "diplotypes": [
2763 { 2987 {
2764 "name": "*1/*1", 2988 "name": "*1/*1",
2815 }, 3039 },
2816 "uncallableHaplotypes": [], 3040 "uncallableHaplotypes": [],
2817 "ignoredHaplotypes": [] 3041 "ignoredHaplotypes": []
2818 }, 3042 },
2819 { 3043 {
2820 "alleleDefinitionVersion": "01/10/22", 3044 "alleleDefinitionVersion": "04/20/22",
2821 "chromosome": "chr16", 3045 "chromosome": "chr16",
2822 "gene": "VKORC1", 3046 "gene": "VKORC1",
2823 "diplotypes": [ 3047 "diplotypes": [
2824 { 3048 {
2825 "name": "rs9923231 reference (C)/rs9923231 reference (C)", 3049 "name": "rs9923231 reference (C)/rs9923231 reference (C)",