2020Fall.json

{"paragraphs":[{"text":"%md\n# Major questions\n1. Is it possible to upload a list of hg38 chromosome/position/ref/alt combinations (e.g. `chr2\\t31529398\\tC\\tT\\n`) from my local computer and look them up in the current Variant WorkBench (VWB)? If so, what input format/script are needed?\n    YG: Sent a list of variants\n2. Similar to above, what if I have a list of gene symbols and NCBI Entrez Gene IDs (e.g. `AKT1\\t207\\nAPC2\\t10297\\n`)?\n    YG: Sent a list of genes\n3. For cohorts with trio germline variants: what are parental status of the germline variants, are they inherited (from either parent) or de novo? If inherited, does zygosity match Mendelian inheritance pattern (e.g. dominant, recessive etc.)?\n    JC: can come up with a workaround; will implement full/formal family relationship feature after mid-September webinar\n\n# Minor issues\n1. In table `occurrences`, update column name `is_multi_alellic` to `is_multi_allelic`\n    JC: will update\n2. ~~In `occurrences` and all other tables, can we have `chromosome` as the first column instead of the last?~~\n    JC: too complicated to update; stay as is\n","user":"Yiran Guo","dateUpdated":"2020-10-06T14:39:26+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h1>Major questions</h1>\n<ol>\n  <li>Is it possible to upload a list of hg38 chromosome/position/ref/alt combinations (e.g. <code>chr2\\t31529398\\tC\\tT\\n</code>) from my local computer and look them up in the current Variant WorkBench (VWB)? If so, what input format/script are needed?<br/>YG: Sent a list of variants</li>\n  <li>Similar to above, what if I have a list of gene symbols and NCBI Entrez Gene IDs (e.g. <code>AKT1\\t207\\nAPC2\\t10297\\n</code>)?<br/>YG: Sent a list of genes</li>\n  <li>For cohorts with trio germline variants: what are parental status of the germline variants, are they inherited (from either parent) or de novo? If inherited, does zygosity match Mendelian inheritance pattern (e.g. dominant, recessive etc.)?<br/>JC: can come up with a workaround; will implement full/formal family relationship feature after mid-September webinar</li>\n</ol>\n<h1>Minor issues</h1>\n<ol>\n  <li>In table <code>occurrences</code>, update column name <code>is_multi_alellic</code> to <code>is_multi_allelic</code><br/>JC: will update</li>\n  <li><del>In <code>occurrences</code> and all other tables, can we have <code>chromosome</code> as the first column instead of the last?</del><br/>JC: too complicated to update; stay as is</li>\n</ol>\n</div>"}]},"apps":[],"jobName":"paragraph_1599746990936_-810178158","id":"20200910-140950_1711497313","dateCreated":"2020-09-10T14:09:50+0000","dateStarted":"2020-10-06T14:39:27+0000","dateFinished":"2020-10-06T14:39:27+0000","status":"FINISHED","progressUpdateIntervalMs":500,"focus":true,"$$hashKey":"object:42302"},{"text":"%sql\nSELECT study_id, count(study_id) FROM occurrences GROUP BY study_id","user":"Yiran Guo","dateUpdated":"2020-10-06T14:39:27+0000","config":{"colWidth":4,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":250,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"study_id":"string","count(study_id)":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}},"1":{"graph":{"mode":"table","height":86,"optionOpen":false}}},"editorSetting":{"language":"sql","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/sql"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"study_id\tcount(study_id)\nSD_6FPYJQBR\t2128264232\nSD_9PYZAHHE\t8091474542\nSD_DZTB5HRR\t5868475127\nSD_PREASA7S\t15630781416\nSD_BHJXBDQK\t12227001\nSD_YGVA0E1C\t6248956483\n"},{"type":"TEXT","data":""}]},"apps":[],"jobName":"paragraph_1600910756705_1975277173","id":"20200924-012556_1862048117","dateCreated":"2020-09-24T01:25:56+0000","dateStarted":"2020-10-06T14:39:27+0000","dateFinished":"2020-10-06T14:47:43+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42303"},{"text":"%sql\nselect count(*) from studies where study_id='SD_BHJXBDQK'","user":"Yiran Guo","dateUpdated":"2020-10-06T14:47:43+0000","config":{"colWidth":4,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":250,"optionOpen":false,"setting":{"table":{"tableGridState":{"columns":[{"name":"attribution","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"created_at","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"data_access_authority","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"external_id","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"kf_id","visible":true,"width":"*","sort":{},"filters":[{"term":"SD_BHJXBDQK"}],"pinned":""},{"name":"modified_at","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"name","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"participants","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"release_status","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"study_files","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"version","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"short_name","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"visible","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"study_id","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"release_id","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""}],"scrollFocus":{},"selection":[],"grouping":{"grouping":[],"aggregations":[],"rowExpandedStates":{}},"treeView":{},"pagination":{"paginationCurrentPage":1,"paginationPageSize":250}},"tableColumnTypeState":{"names":{"count(1)":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":true,"showPagination":true,"showAggregationFooter":true},"updated":false,"initialized":false}},"commonSetting":{}}},"1":{"graph":{"mode":"table","height":86,"optionOpen":false}}},"editorSetting":{"language":"sql","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/sql"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"count(1)\n62\n"},{"type":"TEXT","data":""}]},"apps":[],"jobName":"paragraph_1601496207624_1177204812","id":"20200930-200327_1148767600","dateCreated":"2020-09-30T20:03:27+0000","dateStarted":"2020-10-06T14:47:43+0000","dateFinished":"2020-10-06T14:47:44+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42304"},{"text":"%sql\nselect count(*) from studies where kf_id='SD_BHJXBDQK'","user":"Yiran Guo","dateUpdated":"2020-10-06T14:47:44+0000","config":{"colWidth":4,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":250,"optionOpen":false,"setting":{"table":{"tableGridState":{"columns":[{"name":"attribution","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"created_at","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"data_access_authority","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"external_id","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"kf_id","visible":true,"width":"*","sort":{},"filters":[{"term":"SD_BHJXBDQK"}],"pinned":""},{"name":"modified_at","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"name","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"participants","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"release_status","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"study_files","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"version","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"short_name","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"visible","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"study_id","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""},{"name":"release_id","visible":true,"width":"*","sort":{},"filters":[{}],"pinned":""}],"scrollFocus":{},"selection":[],"grouping":{"grouping":[],"aggregations":[],"rowExpandedStates":{}},"treeView":{},"pagination":{"paginationCurrentPage":1,"paginationPageSize":250}},"tableColumnTypeState":{"names":{"count(1)":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":true,"showPagination":true,"showAggregationFooter":true},"updated":false,"initialized":false}},"commonSetting":{}}},"1":{"graph":{"mode":"table","height":96,"optionOpen":false}}},"editorSetting":{"language":"sql","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/sql","editorHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"count(1)\n11\n"},{"type":"TEXT","data":""}]},"apps":[],"jobName":"paragraph_1601575784711_2130753061","id":"20201001-180944_517183593","dateCreated":"2020-10-01T18:09:44+0000","dateStarted":"2020-10-06T14:47:44+0000","dateFinished":"2020-10-06T14:47:45+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42305"},{"text":"%md\n# Retrieve \"all\" *NOTCH1* variants in `PT_ZYKASPCW`\nWithout knowing the specific chromosome/positions of this gene or the specific study this patient belongs to. (This is a request made by Allison as an example.)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:47:45+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h1>Retrieve &ldquo;all&rdquo; <em>NOTCH1</em> variants in <code>PT_ZYKASPCW</code></h1>\n<p>Without knowing the specific chromosome/positions of this gene or the specific study this patient belongs to. (This is a request made by Allison as an example.)</p>\n</div>"}]},"apps":[],"jobName":"paragraph_1600915314292_1507649033","id":"20200924-024154_1508136013","dateCreated":"2020-09-24T02:41:54+0000","dateStarted":"2020-10-06T14:47:45+0000","dateFinished":"2020-10-06T14:47:45+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42306"},{"text":"%pyspark\nparticipant_id = 'PT_ZYKASPCW'\ngene_symbol = 'NOTCH1'\nstudy_id = spark.sql(\"select study_id from participants where kf_id = '\" + participant_id + \"'\").collect()[0]['study_id']\nchr = spark.sql(\"select chromosome from human_genes where symbol='\" + gene_symbol + \"'\").collect()[0]['chromosome']\nc = spark.sql(\"select distinct chromosome, start, reference, alternate from consequences c where c.symbol='\" + gene_symbol + \"' and c.chromosome=\" + chr)\no = spark.table('occurrences').alias('o')\no = o.where((o['chromosome'] == chr) & (o['study_id'] == study_id) & (o['participant_id'] == participant_id))\nr = o.join(c, (o['chromosome'] == c['chromosome']) & (o['start'] == c['start']) & (o['reference'] == c['reference']) & (o['alternate'] == c['alternate']))\nz.show(r.select('o.*'))","user":"Yiran Guo","dateUpdated":"2020-10-06T14:47:45+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":300,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}}},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python","editorHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"start\tend\treference\talternate\tname\tad\tdp\tgq\tcalls\thas_alt\tis_multi_alellic\told_multi_allelic\trelease_id\thgvsg\tvariant_class\tbiospecimen_id\tparticipant_id\tfamily_id\tbucket\tstudy_id\tdbgap_consent_code\tchromosome\n136490154\t136490169\tCTTTTTTTTTTTTTT\tC\trs71384084\tWrappedArray(7, 0)\t7\t20\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136490176_136490189del\tdeletion\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136514304\t136514305\tA\tG\trs3125005\tWrappedArray(14, 6)\t20\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136514304A>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136537267\t136537268\tG\tA\trs3013301\tWrappedArray(17, 11)\t28\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136537267G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136524699\t136524700\tG\tA\trs138159889\tWrappedArray(16, 0)\t16\t25\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136524699G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136516922\t136516923\tA\tG\trs3125007\tWrappedArray(12, 17)\t29\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136516922A>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136549650\t136549651\tC\tT\trs1058233\tWrappedArray(13, 19)\t32\t99\tWrappedArray(0, 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1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136533313_136533314insCG\tinsertion\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136511049\t136511050\tA\tG\trs9411206\tWrappedArray(9, 16)\t25\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136511049A>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136516651\t136516652\tA\tC\trs3124604\tWrappedArray(14, 9)\t23\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136516651A>C\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136549639\t136549640\tA\tG\trs1058232\tWrappedArray(14, 18)\t32\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136549639A>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136517262\t136517263\tT\tC\trs11145767\tWrappedArray(8, 20)\t28\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136517262T>C\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136497184\t136497185\tG\tA\trs2229974\tWrappedArray(31, 0)\t31\t71\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136497184G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136515737\t136515738\tG\tC\tnull\tWrappedArray(20, 11)\t31\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136515737G>C\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136501450\t136501451\tG\tGA\trs7850324\tWrappedArray(0, 25)\t25\t43\tWrappedArray(1, 1)\ttrue\ttrue\tchr9:136501450:G/GA/A\tRE_000006\tchr9:g.136501451_136501450insA\tindel\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136517170\t136517171\tG\tA\trs10781498\tWrappedArray(9, 8)\t17\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136517170G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136546393\t136546394\tG\tA\trs3013306\tWrappedArray(21, 29)\t50\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136546393G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136519456\t136519457\tC\tT\trs2229975\tWrappedArray(13, 17)\t30\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136519456C>T\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136529443\t136529444\tC\tT\trs4265307\tWrappedArray(10, 16)\t26\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136529443C>T\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136549235\t136549236\tG\tT\trs11792084\tWrappedArray(8, 15)\t23\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136549235G>T\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136494519\t136494520\tT\tC\tnull\tWrappedArray(22, 0)\t22\t63\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136494519T>C\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136533458\t136533459\tC\tT\trs13294808\tWrappedArray(17, 12)\t29\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136533458C>T\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136501439\t136501440\tC\tCA\tnull\tWrappedArray(9, 10)\t19\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136501449dup\tinsertion\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136502974\t136502975\tG\tA\trs11574905\tWrappedArray(11, 18)\t29\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136502974G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136529891\t136529892\tG\tA\trs10870079\tWrappedArray(17, 12)\t29\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136529891G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136490069\t136490070\tT\tG\trs13283788\tWrappedArray(37, 0)\t37\t99\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136490069T>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136501956\t136501957\tA\tG\trs3124594\tWrappedArray(22, 0)\t22\t23\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136501956A>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136519081\t136519082\tC\tT\trs9411209\tWrappedArray(24, 7)\t31\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136519081C>T\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136498723\t136498724\tA\tG\trs3124593\tWrappedArray(23, 0)\t23\t25\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136498723A>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136537422\t136537423\tG\tA\trs3013302\tWrappedArray(14, 15)\t29\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136537422G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136527096\t136527097\tG\tA\trs11574863\tWrappedArray(11, 9)\t20\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136527096G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136516137\t136516138\tA\tG\trs4880099\tWrappedArray(14, 13)\t27\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136516137A>G\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136524639\t136524641\tCT\tC\trs72104354\tWrappedArray(18, 3)\t21\t7\tWrappedArray(0, 0)\tfalse\ttrue\tchr9:136524639:CT/C/*\tRE_000006\tnull\tnull\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136528437\t136528438\tG\tA\trs78789615\tWrappedArray(5, 1)\t6\t63\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136528437G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136519192\t136519193\tC\tT\trs146264157\tWrappedArray(14, 20)\t34\t99\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136519192C>T\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136543953\t136543954\tC\tT\trs143229795\tWrappedArray(20, 0)\t20\t80\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136543953C>T\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136501450\t136501451\tG\tA\trs7850324\tWrappedArray(0, 0)\t25\t43\tWrappedArray(-1, -1)\tfalse\ttrue\tchr9:136501450:G/GA/A\tRE_000006\tchr9:g.136501450G>A\tindel\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136550185\t136550186\tG\tA\trs1110126\tWrappedArray(0, 18)\t18\t99\tWrappedArray(1, 1)\ttrue\tfalse\tnull\tRE_000006\tchr9:g.136550185G>A\tSNV\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n136510510\t136510512\tTC\tT\trs147437562\tWrappedArray(40, 0)\t40\t99\tWrappedArray(0, 0)\tfalse\tfalse\tnull\tRE_000006\tchr9:g.136510515del\tdeletion\tBS_BBV8D7ST\tPT_ZYKASPCW\tFM_6M7B01P0\t8\tSD_PREASA7S\tphs001138.c1\t9\n"},{"type":"TEXT","data":"\n"}]},"apps":[],"jobName":"paragraph_1600908930193_2047225375","id":"20200924-005530_1541857157","dateCreated":"2020-09-24T00:55:30+0000","dateStarted":"2020-10-06T14:47:45+0000","dateFinished":"2020-10-06T14:52:10+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42307"},{"text":"%md\n# Retrieve specific variants of interest in Kids First cohorts that I have access to\nThe following 7 variants are from Table 1 of the 2019 Nature Medicine [paper](https://www.nature.com/articles/s41591-019-0479-2) with PuBMed ID [31263281](https://pubmed.ncbi.nlm.nih.gov/31263281/), see table below.\nFirst I converted transcript-specific, HGVS-format variants (mutations) into chromosomal coordinates in hg38 using [Mutalyzer](https://www.mutalyzer.nl/), then generate notebook codes for variant lookup\n\n(It seems the study `SD_BHJXBDQK` contains somatic variants from tumor DNA in CBTN)\n\n![here](http://127.0.0.1/~guoy/NatMed_paper_table1.png)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:52:10+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h1>Retrieve specific variants of interest in Kids First cohorts that I have access to</h1>\n<p>The following 7 variants are from Table 1 of the 2019 Nature Medicine <a href=\"https://www.nature.com/articles/s41591-019-0479-2\">paper</a> with PuBMed ID <a href=\"https://pubmed.ncbi.nlm.nih.gov/31263281/\">31263281</a>, see table below.<br/>First I converted transcript-specific, HGVS-format variants (mutations) into chromosomal coordinates in hg38 using <a href=\"https://www.mutalyzer.nl/\">Mutalyzer</a>, then generate notebook codes for variant lookup</p>\n<p>(It seems the study <code>SD_BHJXBDQK</code> contains somatic variants from tumor DNA in CBTN)</p>\n<p><img src=\"http://127.0.0.1/~guoy/NatMed_paper_table1.png\" alt=\"here\" /></p>\n</div>"}]},"apps":[],"jobName":"paragraph_1600958823467_-401797155","id":"20200924-144703_1370901230","dateCreated":"2020-09-24T14:47:03+0000","dateStarted":"2020-10-06T14:52:11+0000","dateFinished":"2020-10-06T14:52:11+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42308"},{"text":"%md\n## *KRAS* variant `NM_004985.4:c.35G>A:p.G12D`","user":"Yiran Guo","dateUpdated":"2020-10-06T14:52:11+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h2><em>KRAS</em> variant <code>NM_004985.4:c.35G&gt;A:p.G12D</code></h2>\n</div>"}]},"apps":[],"jobName":"paragraph_1601495736440_-1476113924","id":"20200930-195536_257261326","dateCreated":"2020-09-30T19:55:36+0000","dateStarted":"2020-10-06T14:52:11+0000","dateFinished":"2020-10-06T14:52:11+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42309"},{"text":"%pyspark\ngene_symbol = 'KRAS'\nchr = 12\nstart = 25245350\nend = 25245351\no = spark.table('occurrences').alias('o')\nr = o.where((o['chromosome'] == chr) & (o['start'] == start) & (o['end'] == end))\nz.show(r)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:52:11+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":300,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}}},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"start\tend\treference\talternate\tname\tad\tdp\tgq\tcalls\thas_alt\tis_multi_alellic\told_multi_allelic\trelease_id\thgvsg\tvariant_class\tbiospecimen_id\tparticipant_id\tfamily_id\tbucket\tstudy_id\tdbgap_consent_code\tchromosome\n25245350\t25245351\tC\tT\tnull\tWrappedArray(52, 14)\t66\tnull\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tnull\tnull\tBS_94AP61Q5\tPT_DDFAZ345\tnull\t2\tSD_BHJXBDQK\tSD_BHJXBDQK.c1\t12\n25245350\t25245351\tC\tG\tnull\tWrappedArray(57, 0)\t57\tnull\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tnull\tnull\tBS_QGEEVNAS\tPT_NNZQ09SH\tnull\t2\tSD_BHJXBDQK\tSD_BHJXBDQK.c1\t12\n25245350\t25245351\tC\tA\tnull\tWrappedArray(40, 7)\t47\tnull\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tnull\tnull\tBS_JM979K1M\tPT_1TB2V1PH\tnull\t2\tSD_BHJXBDQK\tSD_BHJXBDQK.c1\t12\n25245350\t25245351\tC\tT\tnull\tWrappedArray(75, 16)\t91\tnull\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tnull\tnull\tBS_KV3XF9WV\tPT_GBDYKSPY\tnull\t2\tSD_BHJXBDQK\tSD_BHJXBDQK.c1\t12\n25245350\t25245351\tC\tT\tnull\tWrappedArray(66, 6)\t72\tnull\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tnull\tnull\tBS_Z14Z2JMW\tPT_9ZY739FB\tnull\t2\tSD_BHJXBDQK\tSD_BHJXBDQK.c1\t12\n"},{"type":"TEXT","data":"\n"}]},"apps":[],"jobName":"paragraph_1601495639377_491424397","id":"20200930-195359_1597505716","dateCreated":"2020-09-30T19:53:59+0000","dateStarted":"2020-10-06T14:52:11+0000","dateFinished":"2020-10-06T14:53:36+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42310"},{"text":"%md\n## *BRAF* variant `NM_004333.4:c.1403T>C:p.F468S`\n","user":"Yiran Guo","dateUpdated":"2020-10-06T14:53:36+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h2><em>BRAF</em> variant <code>NM_004333.4:c.1403T&gt;C:p.F468S</code></h2>\n</div>"}]},"apps":[],"jobName":"paragraph_1601576555349_1488001099","id":"20201001-182235_1523062088","dateCreated":"2020-10-01T18:22:35+0000","dateStarted":"2020-10-06T14:53:36+0000","dateFinished":"2020-10-06T14:53:36+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42311"},{"text":"%pyspark\no = spark.table('occurrences').alias('o')\nchr = 7\nstart = 140781605\nend = 140781606\nr = o.where((o['chromosome'] == chr) & (o['start'] == start) & (o['end'] == end))\nz.show(r)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:53:36+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":98,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}}},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"start\tend\treference\talternate\tname\tad\tdp\tgq\tcalls\thas_alt\tis_multi_alellic\told_multi_allelic\trelease_id\thgvsg\tvariant_class\tbiospecimen_id\tparticipant_id\tfamily_id\tbucket\tstudy_id\tdbgap_consent_code\tchromosome\n"},{"type":"TEXT","data":"\n"}]},"apps":[],"jobName":"paragraph_1601927501558_-912050911","id":"20201005-195141_1115092813","dateCreated":"2020-10-05T19:51:41+0000","dateStarted":"2020-10-06T14:53:36+0000","dateFinished":"2020-10-06T14:54:16+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42312"},{"text":"%md\n## *RASA1* variant `NM_002890.2:c.475_476del:p.L159Gfs*20`","user":"Yiran Guo","dateUpdated":"2020-10-06T14:54:16+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h2><em>RASA1</em> variant <code>NM_002890.2:c.475_476del:p.L159Gfs*20</code></h2>\n</div>"}]},"apps":[],"jobName":"paragraph_1601927520954_-1987239058","id":"20201005-195200_1673922054","dateCreated":"2020-10-05T19:52:00+0000","dateStarted":"2020-10-06T14:54:16+0000","dateFinished":"2020-10-06T14:54:16+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42313"},{"text":"%pyspark\no = spark.table('occurrences').alias('o')\nchr = 5\nstart = 87268926\nend = 87268928\nr = o.where((o['chromosome'] == chr) & (o['start'] == start) & (o['end'] == end))\nz.show(r)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:54:17+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":94,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}}},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"start\tend\treference\talternate\tname\tad\tdp\tgq\tcalls\thas_alt\tis_multi_alellic\told_multi_allelic\trelease_id\thgvsg\tvariant_class\tbiospecimen_id\tparticipant_id\tfamily_id\tbucket\tstudy_id\tdbgap_consent_code\tchromosome\n"},{"type":"TEXT","data":"\n"}]},"apps":[],"jobName":"paragraph_1601927537710_-1562447713","id":"20201005-195217_1826328027","dateCreated":"2020-10-05T19:52:17+0000","dateStarted":"2020-10-06T14:54:17+0000","dateFinished":"2020-10-06T14:55:34+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42314"},{"text":"%md\n## *SOS1* variant `NM_005633.3:c.2536G>A:p.E846K`","user":"Yiran Guo","dateUpdated":"2020-10-06T14:55:34+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h2><em>SOS1</em> variant <code>NM_005633.3:c.2536G&gt;A:p.E846K</code></h2>\n</div>"}]},"apps":[],"jobName":"paragraph_1601927555251_-2042087677","id":"20201005-195235_803991629","dateCreated":"2020-10-05T19:52:35+0000","dateStarted":"2020-10-06T14:55:34+0000","dateFinished":"2020-10-06T14:55:34+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42315"},{"text":"%pyspark\no = spark.table('occurrences').alias('o')\nchr = 2\nstart = 39007168\nend = 39007169\nr = o.where((o['chromosome'] == chr) & (o['start'] == start) & (o['end'] == end))\nz.show(r)\nprint(r['biospecimen_id'])","user":"Yiran Guo","dateUpdated":"2020-10-06T14:55:34+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":134,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}}},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"start\tend\treference\talternate\tname\tad\tdp\tgq\tcalls\thas_alt\tis_multi_alellic\told_multi_allelic\trelease_id\thgvsg\tvariant_class\tbiospecimen_id\tparticipant_id\tfamily_id\tbucket\tstudy_id\tdbgap_consent_code\tchromosome\n39007168\t39007169\tC\tT\tnull\tWrappedArray(53, 31)\t84\tnull\tWrappedArray(0, 1)\ttrue\tfalse\tnull\tRE_000006\tnull\tnull\tBS_MRX1SPFB\tPT_H024RK87\tnull\t2\tSD_BHJXBDQK\tSD_BHJXBDQK.c1\t2\n"},{"type":"TEXT","data":"\nColumn<b'biospecimen_id'>\n"}]},"apps":[],"jobName":"paragraph_1601927571104_946181176","id":"20201005-195251_339765949","dateCreated":"2020-10-05T19:52:51+0000","dateStarted":"2020-10-06T14:55:34+0000","dateFinished":"2020-10-06T14:57:08+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42316"},{"text":"%python\nimport requests\nimport json\nr = requests.get('https://kf-api-dataservice.kidsfirstdrc.org/biospecimens/BS_MRX1SPFB')\nprint(json.dumps(r.json(), indent=2))","user":"Yiran Guo","dateUpdated":"2020-10-06T14:57:08+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TEXT","data":"{\n  \"_status\": {\n    \"message\": \"success\", \n    \"code\": 200\n  }, \n  \"_links\": {\n    \"diagnoses\": \"/diagnoses?biospecimen_id=BS_MRX1SPFB\", \n    \"participant\": \"/participants/PT_H024RK87\", \n    \"self\": \"/biospecimens/BS_MRX1SPFB\", \n    \"collection\": \"/biospecimens\", \n    \"biospecimen_diagnoses\": \"/biospecimen-diagnoses?biospecimen_id=BS_MRX1SPFB\", \n    \"biospecimen_genomic_files\": \"/biospecimen-genomic-files?biospecimen_id=BS_MRX1SPFB\", \n    \"sequencing_center\": \"/sequencing-centers/SC_N1EVHSME\", \n    \"genomic_files\": \"/genomic-files?biospecimen_id=BS_MRX1SPFB\"\n  }, \n  \"results\": {\n    \"volume_ul\": null, \n    \"source_text_tissue_type\": \"Tumor\", \n    \"ncit_id_tissue_type\": \"NCIT:C18009\", \n    \"analyte_type\": \"DNA\", \n    \"visible\": true, \n    \"consent_type\": \"GRU\", \n    \"external_aliquot_id\": \"717047\", \n    \"concentration_mg_per_ml\": 0.0181, \n    \"duo_ids\": null, \n    \"shipment_date\": null, \n    \"source_text_tumor_descriptor\": \"Recurrence\", \n    \"spatial_descriptor\": null, \n    \"age_at_event_days\": 5870, \n    \"external_sample_id\": \"7316-104-T-69547.WGS\", \n    \"method_of_sample_procurement\": null, \n    \"uberon_id_anatomical_site\": \"UBERON:0001017\", \n    \"kf_id\": \"BS_MRX1SPFB\", \n    \"dbgap_consent_code\": \"SD_BHJXBDQK.c1\", \n    \"created_at\": \"2018-08-14T15:20:08.082626+00:00\", \n    \"modified_at\": \"2019-09-30T22:22:28.323361+00:00\", \n    \"composition\": \"Solid Tissue\", \n    \"source_text_anatomical_site\": \"Central Nervous System\", \n    \"ncit_id_anatomical_site\": \"NCIT:C12438\", \n    \"shipment_origin\": null\n  }\n}\n"}]},"apps":[],"jobName":"paragraph_1601927653555_-2034554910","id":"20201005-195413_570414175","dateCreated":"2020-10-05T19:54:13+0000","dateStarted":"2020-10-06T14:57:08+0000","dateFinished":"2020-10-06T14:57:08+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42317"},{"text":"%md\n## *PTPN11* variant `NM_002834.3:c.1504T>G:p.S502A`","user":"Yiran Guo","dateUpdated":"2020-10-06T14:57:08+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h2><em>PTPN11</em> variant <code>NM_002834.3:c.1504T&gt;G:p.S502A</code></h2>\n</div>"}]},"apps":[],"jobName":"paragraph_1601927590635_-1280603184","id":"20201005-195310_2124420976","dateCreated":"2020-10-05T19:53:10+0000","dateStarted":"2020-10-06T14:57:08+0000","dateFinished":"2020-10-06T14:57:08+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42318"},{"text":"%pyspark\no = spark.table('occurrences').alias('o')\nchr = 12\nstart = 112489080\nend = 112489081\nr = o.where((o['chromosome'] == chr) & (o['start'] == start) & (o['end'] == end))\nz.show(r)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:57:08+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":88,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}}},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"start\tend\treference\talternate\tname\tad\tdp\tgq\tcalls\thas_alt\tis_multi_alellic\told_multi_allelic\trelease_id\thgvsg\tvariant_class\tbiospecimen_id\tparticipant_id\tfamily_id\tbucket\tstudy_id\tdbgap_consent_code\tchromosome\n"},{"type":"TEXT","data":"\n"}]},"apps":[],"jobName":"paragraph_1601927601154_1230541741","id":"20201005-195321_299538796","dateCreated":"2020-10-05T19:53:21+0000","dateStarted":"2020-10-06T14:57:08+0000","dateFinished":"2020-10-06T14:58:20+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42319"},{"text":"%md\n## *PTPN11* variant `NM_002834.3:c.1510A>G:p.M504V`","user":"Yiran Guo","dateUpdated":"2020-10-06T14:58:20+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h2><em>PTPN11</em> variant <code>NM_002834.3:c.1510A&gt;G:p.M504V</code></h2>\n</div>"}]},"apps":[],"jobName":"paragraph_1601927613019_1018301132","id":"20201005-195333_369244002","dateCreated":"2020-10-05T19:53:33+0000","dateStarted":"2020-10-06T14:58:20+0000","dateFinished":"2020-10-06T14:58:20+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42320"},{"text":"%pyspark\no = spark.table('occurrences').alias('o')\nchr = 12\nstart = 112489086\nend = 112489087\nr = o.where((o['chromosome'] == chr) & (o['start'] == start) & (o['end'] == end))\nz.show(r)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:58:20+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":84,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for columns\"},{\"name\":\"showPagination\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable pagination for better navigation\"},{\"name\":\"showAggregationFooter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable a footer for displaying aggregated values\"}]","tableOptionValue":{"useFilter":false,"showPagination":false,"showAggregationFooter":false},"updated":false,"initialized":false}},"commonSetting":{}}}},"editorSetting":{"language":"python","editOnDblClick":false,"completionKey":"TAB","completionSupport":true},"editorMode":"ace/mode/python"},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"TABLE","data":"start\tend\treference\talternate\tname\tad\tdp\tgq\tcalls\thas_alt\tis_multi_alellic\told_multi_allelic\trelease_id\thgvsg\tvariant_class\tbiospecimen_id\tparticipant_id\tfamily_id\tbucket\tstudy_id\tdbgap_consent_code\tchromosome\n"},{"type":"TEXT","data":"\n"}]},"apps":[],"jobName":"paragraph_1601927624241_-2002170922","id":"20201005-195344_4893115","dateCreated":"2020-10-05T19:53:44+0000","dateStarted":"2020-10-06T14:58:20+0000","dateFinished":"2020-10-06T14:59:32+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42321"},{"text":"%md\n## *PTPN11* variant `NM_002834.3:c.1530G>C:p.Q510H`","user":"Yiran Guo","dateUpdated":"2020-10-06T14:59:32+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{},"editorSetting":{"language":"markdown","editOnDblClick":true,"completionKey":"TAB","completionSupport":false},"editorMode":"ace/mode/markdown","editorHide":true,"tableHide":false},"settings":{"params":{},"forms":{}},"results":{"code":"SUCCESS","msg":[{"type":"HTML","data":"<div class=\"markdown-body\">\n<h2><em>PTPN11</em> variant <code>NM_002834.3:c.1530G&gt;C:p.Q510H</code></h2>\n</div>"}]},"apps":[],"jobName":"paragraph_1601927633073_-939380210","id":"20201005-195353_1695257998","dateCreated":"2020-10-05T19:53:53+0000","dateStarted":"2020-10-06T14:59:32+0000","dateFinished":"2020-10-06T14:59:32+0000","status":"FINISHED","progressUpdateIntervalMs":500,"$$hashKey":"object:42322"},{"text":"%pyspark\no = spark.table('occurrences').alias('o')\nchr = 12\nstart = 112489106\nend = 112489107\nr = o.where((o['chromosome'] == chr) & (o['start'] == start) & (o['end'] == end))\nz.show(r)","user":"Yiran Guo","dateUpdated":"2020-10-06T14:59:32+0000","config":{"colWidth":12,"fontSize":9,"enabled":true,"results":{"0":{"graph":{"mode":"table","height":84,"optionOpen":false,"setting":{"table":{"tableGridState":{},"tableColumnTypeState":{"names":{"start":"string","end":"string","reference":"string","alternate":"string","name":"string","ad":"string","dp":"string","gq":"string","calls":"string","has_alt":"string","is_multi_alellic":"string","old_multi_allelic":"string","release_id":"string","hgvsg":"string","variant_class":"string","biospecimen_id":"string","participant_id":"string","family_id":"string","bucket":"string","study_id":"string","dbgap_consent_code":"string","chromosome":"string"},"updated":false},"tableOptionSpecHash":"[{\"name\":\"useFilter\",\"valueType\":\"boolean\",\"defaultValue\":false,\"widget\":\"checkbox\",\"description\":\"Enable filter for 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