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and drop your file (or upload from your computer).",{"type":431,"tag":432,"props":695,"children":696},{},[697],{"type":476,"value":698},"OR",{"type":431,"tag":626,"props":700,"children":702},{"start":701},4,[703],{"type":431,"tag":630,"props":704,"children":705},{},[706],{"type":476,"value":707},"Click \"Single Variant\" tab and choose whether you want to input a SNV, INDEL or HGVS annotation.",{"type":431,"tag":596,"props":709,"children":711},{"id":710},"advanced-options-available-only-with-vcf-files",[712],{"type":476,"value":713},"Advanced options (available only with VCF files)",{"type":431,"tag":432,"props":715,"children":716},{},[717],{"type":476,"value":718},"The \"Advanced option\" panel lets you customize the behavior of the pipeline for your VCF file only:",{"type":431,"tag":720,"props":721,"children":722},"ul",{},[723,735,740],{"type":431,"tag":630,"props":724,"children":725},{},[726,728,733],{"type":476,"value":727},"Gene list: Pick a gene list from the dropdown.\nThis 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lines.",{"type":431,"tag":630,"props":741,"children":742},{},[743],{"type":476,"value":744},"Max Population frequency: PIE by default will not call medals for variants present in the ExAC (ex-TCGA) database at an allele frequency greater than 0.001.\nThis option lets you override the filtering threshold to whatever frequency you prefer.\nTo disable filtering altogether, specify a value of 1.",{"type":431,"tag":596,"props":746,"children":748},{"id":747},"progress-page",[749],{"type":476,"value":750},"Progress page",{"type":431,"tag":432,"props":752,"children":753},{},[754],{"type":476,"value":755},"After uploading is complete you will be taken to a status screen showing the progress of your job through the system.\nAnalysis typically takes 10-15 minutes depending on file size and system availability.",{"type":431,"tag":432,"props":757,"children":758},{},[759],{"type":476,"value":760},"It isn't necessary to keep your browser open on this page until your results are ready: the system will e-mail you with a link to return to your results.\nOptional browser notifications are also available.",{"type":431,"tag":596,"props":762,"children":764},{"id":763},"analysis-of-results",[765],{"type":476,"value":766},"Analysis of Results",{"type":431,"tag":619,"props":768,"children":770},{"id":769},"results-browser",[771],{"type":476,"value":772},"Results browser",{"type":431,"tag":432,"props":774,"children":775},{},[776],{"type":476,"value":777},"When your job is complete you will be taken to an overview page where you can browse your results and examine a detailed results page for each variant.\nEach header can be clicked for sorting.",{"type":431,"tag":432,"props":779,"children":780},{},[781],{"type":431,"tag":436,"props":782,"children":785},{"alt":783,"src":784},"dashboard","/img/pecan/pecan-pie/what-is-pie/pie.png",[],{"type":431,"tag":432,"props":787,"children":788},{},[789],{"type":476,"value":790},"The variants in the results can be filtered by:",{"type":431,"tag":442,"props":792,"children":793},{},[794,810],{"type":431,"tag":446,"props":795,"children":796},{},[797],{"type":431,"tag":450,"props":798,"children":799},{},[800,805],{"type":431,"tag":454,"props":801,"children":802},{},[803],{"type":476,"value":804},"Filter",{"type":431,"tag":454,"props":806,"children":807},{},[808],{"type":476,"value":809},"Meaning",{"type":431,"tag":461,"props":811,"children":812},{},[813,826,839,852],{"type":431,"tag":450,"props":814,"children":815},{},[816,821],{"type":431,"tag":468,"props":817,"children":818},{},[819],{"type":476,"value":820},"Class",{"type":431,"tag":468,"props":822,"children":823},{},[824],{"type":476,"value":825},"Predicted effect of variant on protein coding, e.g. missense, nonsense, etc.",{"type":431,"tag":450,"props":827,"children":828},{},[829,834],{"type":431,"tag":468,"props":830,"children":831},{},[832],{"type":476,"value":833},"Somatic medal",{"type":431,"tag":468,"props":835,"children":836},{},[837],{"type":476,"value":838},"Medal assigned to the variant by the somatic classifier.",{"type":431,"tag":450,"props":840,"children":841},{},[842,847],{"type":431,"tag":468,"props":843,"children":844},{},[845],{"type":476,"value":846},"Germline medal",{"type":431,"tag":468,"props":848,"children":849},{},[850],{"type":476,"value":851},"Medal assigned to the variant by the germline classifier.",{"type":431,"tag":450,"props":853,"children":854},{},[855,860],{"type":431,"tag":468,"props":856,"children":857},{},[858],{"type":476,"value":859},"Committee Classification",{"type":431,"tag":468,"props":861,"children":862},{},[863],{"type":476,"value":864},"If the variant has been reviewed by the St. Jude germline variant review committee, the result will appear in this column, otherwise it will be blank.",{"type":431,"tag":432,"props":866,"children":867},{},[868],{"type":476,"value":869},"The \"search\" box lets you filter the results by gene and/or amino acid change.\nThe view is dynamically filtered to matching variants as you type.",{"type":431,"tag":619,"props":871,"children":873},{"id":872},"medal-meaning",[874],{"type":476,"value":875},"Medal meaning",{"type":431,"tag":432,"props":877,"children":878},{},[879],{"type":476,"value":880},"Medals are only assigned for coding and splice-related variants in disease predisposition genes.\nGermline medals are only assigned for novel variants or those present in the ExAC (ex-TCGA) database with a MAF no greater than 0.1% (0.001 expressed fractionally).",{"type":431,"tag":432,"props":882,"children":883},{},[884],{"type":431,"tag":436,"props":885,"children":888},{"alt":886,"src":887},"meadal meaning","/img/pecan/pecan-pie/what-is-pie/Figure2.png",[],{"type":431,"tag":720,"props":890,"children":891},{},[892,902,912],{"type":431,"tag":630,"props":893,"children":894},{},[895,900],{"type":431,"tag":472,"props":896,"children":897},{},[898],{"type":476,"value":899},"Gold medals",{"type":476,"value":901}," are assigned to truncations in tumor suppressor genes, hot spots derived from the COSMIC database, as well as perfect matches to variants in the IARC TP53, PCGP, ASU TERT, ARUP RET, and BIC databases.",{"type":431,"tag":630,"props":903,"children":904},{},[905,910],{"type":431,"tag":472,"props":906,"children":907},{},[908],{"type":476,"value":909},"Silver medals",{"type":476,"value":911}," are assigned to in-frame indels, truncations in non-tumor suppressor genes, variants predicted deleterious by damage-prediction algorithms, variants receiving a gold medal from the somatic classifier, and perfect matches to variants in the following databases: ClinVar (predicted pathogenic or likely pathogenic), RB1, LOVD, and UMD.",{"type":431,"tag":630,"props":913,"children":914},{},[915,920],{"type":431,"tag":472,"props":916,"children":917},{},[918],{"type":476,"value":919},"Bronze medals",{"type":476,"value":921}," are assigned to variants predicted tolerated by damage-prediction algorithms. Variants having an imperfect match to a database (i.e. different variants at the same genomic position or codon) typically receive a lesser medal.",{"type":431,"tag":432,"props":923,"children":924},{},[925,927,932,934,941],{"type":476,"value":926},"A summary graphic can be found in slide 4 of the ASHG 2017 presentation (",{"type":431,"tag":498,"props":928,"children":929},{"href":587,"download":588,"target":589},[930],{"type":476,"value":931},"download here",{"type":476,"value":933},").\nFor additional details see ",{"type":431,"tag":498,"props":935,"children":938},{"href":936,"rel":937},"https://www.nejm.org/doi/full/10.1056/NEJMoa1508054#t=article",[502],[939],{"type":476,"value":940},"Zhang et al., NEJM 2015",{"type":476,"value":942}," (supplementary appendix pp. 7-10).",{"type":431,"tag":619,"props":944,"children":946},{"id":945},"variant-page",[947],{"type":476,"value":948},"Variant page",{"type":431,"tag":432,"props":950,"children":951},{},[952],{"type":476,"value":953},"Each variant links to a detailed variant page, which integrates data from a variety of sources.\nIf either you or the St. Jude germline variant review committee have annotated a variant, that information will be prepopulated.",{"type":431,"tag":955,"props":956,"children":958},"h4",{"id":957},"summary-information",[959],{"type":476,"value":960},"Summary information",{"type":431,"tag":432,"props":962,"children":963},{},[964],{"type":476,"value":965},"The top of the page shows a summary of the variant, including its genomic and HGVS annotations, predicted effect on the protein, and somatic and germline medals.\nA description of the gene from Entrez follows, and a custom description or selection rationale may also be entered.",{"type":431,"tag":955,"props":967,"children":969},{"id":968},"medal-call-information",[970],{"type":476,"value":971},"Medal call information",{"type":431,"tag":432,"props":973,"children":974},{},[975],{"type":476,"value":976},"Clicking on one of the medal icons (gold, silver, bronze, unknown) or on the top of the page will show a summary of information related to the medal call.",{"type":431,"tag":955,"props":978,"children":980},{"id":979},"proteinpaint",[981],{"type":476,"value":308},{"type":431,"tag":432,"props":983,"children":984},{},[985,987,994],{"type":476,"value":986},"An embedded version of ProteinPaint (",{"type":431,"tag":498,"props":988,"children":991},{"href":989,"rel":990},"https://www.nature.com/articles/ng.3466",[502],[992],{"type":476,"value":993},"Zhou et al., Nat. Genet. 2016",{"type":476,"value":995},") appears next, showing the variant in the context of a number of pediatric datasets including PCGP.\nA link is provided to the main ProteinPaint application which provides visualizations for additional datasets, including COSMIC and\nClinVar.",{"type":431,"tag":955,"props":997,"children":999},{"id":998},"ashg-pathogenicity-classification",[1000],{"type":476,"value":1001},"ASHG pathogenicity classification",{"type":431,"tag":432,"props":1003,"children":1004},{},[1005,1007,1014],{"type":476,"value":1006},"Formal variant pathogenicity classification is supported by an interface implementing ACMG guidelines (",{"type":431,"tag":498,"props":1008,"children":1011},{"href":1009,"rel":1010},"https://www.nature.com/gim/journal/v17/n5/full/gim201530a.html",[502],[1012],{"type":476,"value":1013},"Richards et al., Genet Med. 2015",{"type":476,"value":1015},").\nThe analyst reviews a series of curated category tags, assigning applicable tags to the variant and optionally supplying additional information for each such as PubMed IDs and supporting evidence.\nThe system will then compute an appropriate pathogenicity score based on the user-flagged categories.\nAdditional free-form custom evidence can also be entered.\nThis structured approach both helps eliminate arbitrary decision-making from the pathogenicity classification process and also constructs a concise summary of the logic and evidence supporting the final call.",{"type":431,"tag":955,"props":1017,"children":1019},{"id":1018},"clinvar-and-allele-frequency",[1020],{"type":476,"value":1021},"ClinVar and allele frequency",{"type":431,"tag":432,"props":1023,"children":1024},{},[1025],{"type":476,"value":1026},"Matches of the variant in ClinVar are also provided, along with predicted clinical significance and review status.",{"type":431,"tag":432,"props":1028,"children":1029},{},[1030],{"type":476,"value":1031},"Allele frequencies for the variant in the PCGP (somatic and germline), NHLBI ESP 6500, and ExAC databases are presented both as fractional values and on a log10 plot. Detailed allele population breakdowns are provided for ExAC.",{"type":431,"tag":955,"props":1033,"children":1035},{"id":1034},"damage-prediction-algorithms",[1036],{"type":476,"value":1037},"Damage prediction algorithms",{"type":431,"tag":432,"props":1039,"children":1040},{},[1041],{"type":476,"value":1042},"Precomputed damage-prediction algorithm calls for nonsynonymous coding SNVs are presented from the dbNSFP database.\nAvailable algorithms are PolyPhen2 (HVAR), SIFT, CADD, REVEL, FATHMM, MutationAssessor, and LRT.\nThe calls are presented in a circular diagram with entries color-coded based on the predicted severity of the result.",{"type":431,"tag":955,"props":1044,"children":1046},{"id":1045},"medal-ceremony-and-external-links",[1047],{"type":476,"value":1048},"Medal ceremony and external links",{"type":431,"tag":432,"props":1050,"children":1051},{},[1052],{"type":476,"value":1053},"Additional output from medal ceremony classification can also be reviewed.\nThis is only loosely structured, additional fields here may eventually be integrated into Pecan PIE.\nLinks are provided to relevant dbSNP entries and other information sources.",{"type":431,"tag":955,"props":1055,"children":1057},{"id":1056},"final-classification",[1058],{"type":476,"value":1059},"Final classification",{"type":431,"tag":432,"props":1061,"children":1062},{},[1063],{"type":476,"value":1064},"The final 5-tier ACMG classification can be selected after which the decision will be marked as reviewed.\nA checkbox is also available to indicate this variant is a potential candidate for functional review.",{"type":431,"tag":596,"props":1066,"children":1068},{"id":1067},"standalone-usage",[1069],{"type":476,"value":1070},"Standalone usage",{"type":431,"tag":432,"props":1072,"children":1073},{},[1074,1076,1083,1085,1092],{"type":476,"value":1075},"This section is intended only for users who want to invoke Pecan PIE's underlying analysis pipelines independently on the ",{"type":431,"tag":498,"props":1077,"children":1080},{"href":1078,"rel":1079},"https://www.dnanexus.com",[502],[1081],{"type":476,"value":1082},"DNAnexus",{"type":476,"value":1084}," platform.\nIf you just want to use the Pecan PIE website you can safely ignore this section of the documentation.\nWe assume familiarity with the DNAnexus platform.\nIf you aren't familiar with this, DNAnexus' ",{"type":431,"tag":498,"props":1086,"children":1089},{"href":1087,"rel":1088},"https://documentation.dnanexus.com/getting-started/tutorials/cli-quickstart",[502],[1090],{"type":476,"value":1091},"quickstart guide",{"type":476,"value":1093}," is a great place to start.",{"type":431,"tag":1095,"props":1096,"children":1099},"callout",{"color":1097,"icon":1098},"orange","i-heroicons-exclamation-circle",[1100],{"type":431,"tag":432,"props":1101,"children":1102},{},[1103,1108,1112],{"type":431,"tag":472,"props":1104,"children":1105},{},[1106],{"type":476,"value":1107},"Warning",{"type":431,"tag":1109,"props":1110,"children":1111},"br",{},[],{"type":476,"value":1113},"\nThis section of the guide is only relevant to power users!",{"type":431,"tag":432,"props":1115,"children":1116},{},[1117],{"type":476,"value":1118},"Two DNAnexus cloud application pipelines were created during the development of Pecan PIE:",{"type":431,"tag":442,"props":1120,"children":1121},{},[1122,1143],{"type":431,"tag":446,"props":1123,"children":1124},{},[1125],{"type":431,"tag":450,"props":1126,"children":1127},{},[1128,1133,1138],{"type":431,"tag":454,"props":1129,"children":1130},{},[1131],{"type":476,"value":1132},"Name",{"type":431,"tag":454,"props":1134,"children":1135},{},[1136],{"type":476,"value":1137},"Corresponding DNAnexus App",{"type":431,"tag":454,"props":1139,"children":1140},{},[1141],{"type":476,"value":1142},"Description",{"type":431,"tag":461,"props":1144,"children":1145},{},[1146,1178],{"type":431,"tag":450,"props":1147,"children":1148},{},[1149,1154,1164],{"type":431,"tag":468,"props":1150,"children":1151},{},[1152],{"type":476,"value":1153},"VEP+",{"type":431,"tag":468,"props":1155,"children":1156},{},[1157],{"type":431,"tag":498,"props":1158,"children":1161},{"href":1159,"rel":1160},"https://platform.dnanexus.com/app/stjude_vep_plus",[502],[1162],{"type":476,"value":1163},"app-stjude_vep_plus",{"type":431,"tag":468,"props":1165,"children":1166},{},[1167,1169,1176],{"type":476,"value":1168},"A cloud installation of ",{"type":431,"tag":498,"props":1170,"children":1173},{"href":1171,"rel":1172},"https://ensembl.org/info/docs/tools/vep/index.html",[502],[1174],{"type":476,"value":1175},"VEP",{"type":476,"value":1177}," with improved logic for splice variant calls. Converts an input VCF of variants to annotated, tab-delimited format.",{"type":431,"tag":450,"props":1179,"children":1180},{},[1181,1186,1196],{"type":431,"tag":468,"props":1182,"children":1183},{},[1184],{"type":476,"value":1185},"Medal Ceremony",{"type":431,"tag":468,"props":1187,"children":1188},{},[1189],{"type":431,"tag":498,"props":1190,"children":1193},{"href":1191,"rel":1192},"https://platform.dnanexus.com/app/stjude_medal_ceremony",[502],[1194],{"type":476,"value":1195},"app-stjude_medal_ceremony",{"type":431,"tag":468,"props":1197,"children":1198},{},[1199],{"type":476,"value":1200},"Additional annotation and automated variant classification. Requires a special input format which is produced by VEP+.",{"type":431,"tag":619,"props":1202,"children":1204},{"id":1203},"permissions",[1205],{"type":476,"value":1206},"Permissions",{"type":431,"tag":432,"props":1208,"children":1209},{},[1210,1212,1217],{"type":476,"value":1211},"In order to run the cloud pipelines independently, your DNAnexus account needs to be granted permissions to access them.\nAfter your initial login to St. Jude Cloud and/or Pecan PIE, these permissions will be granted automatically.\nA single login is required even if you just want to use the standalone pipelines rather than the Pecan PIE portal (",{"type":431,"tag":498,"props":1213,"children":1214},{"href":522},[1215],{"type":476,"value":1216},"contact us",{"type":476,"value":1218}," if you encounter problems accessing the pipelines).",{"type":431,"tag":432,"props":1220,"children":1221},{},[1222],{"type":476,"value":1223},"There are two methods of running pipelines on DNAnexus:",{"type":431,"tag":626,"props":1225,"children":1226},{},[1227,1237],{"type":431,"tag":630,"props":1228,"children":1229},{},[1230,1235],{"type":431,"tag":472,"props":1231,"children":1232},{},[1233],{"type":476,"value":1234},"DNAnexus GUI.",{"type":476,"value":1236}," DNAnexus provides a standardized graphical user interface for configuring, launching, and monitoring jobs on the cloud.\nOur pipelines can be run like any other DNAnexus pipeline.",{"type":431,"tag":630,"props":1238,"children":1239},{},[1240,1245,1247,1253,1255,1261,1263,1269],{"type":431,"tag":472,"props":1241,"children":1242},{},[1243],{"type":476,"value":1244},"Command line.",{"type":476,"value":1246}," Jobs may also be invoked via the ",{"type":431,"tag":668,"props":1248,"children":1250},{"className":1249},[],[1251],{"type":476,"value":1252},"dx",{"type":476,"value":1254}," command line client.\nCommand-line use allows submitting cloud jobs without interacting with a GUI, and so supports scripting and easier integration with local workflows.\nSee ",{"type":431,"tag":498,"props":1256,"children":1258},{"href":1257},"/genomics-platform/analyzing-data/command-line-interaction#installation",[1259],{"type":476,"value":1260},"this section",{"type":476,"value":1262}," for information on how to get set up with the ",{"type":431,"tag":668,"props":1264,"children":1266},{"className":1265},[],[1267],{"type":476,"value":1268},"dx-toolkit",{"type":476,"value":675},{"type":431,"tag":1095,"props":1271,"children":1274},{"color":1272,"icon":1273},"blue","i-heroicons-document-text-solid",[1275],{"type":431,"tag":432,"props":1276,"children":1277},{},[1278,1283,1286],{"type":431,"tag":472,"props":1279,"children":1280},{},[1281],{"type":476,"value":1282},"Note",{"type":431,"tag":1109,"props":1284,"children":1285},{},[],{"type":476,"value":1287},"\nThe following examples demonstrate command-line usage.",{"type":431,"tag":619,"props":1289,"children":1291},{"id":1290},"uploading-files",[1292],{"type":476,"value":1293},"Uploading files",{"type":431,"tag":432,"props":1295,"children":1296},{},[1297,1299,1305,1307,1314],{"type":476,"value":1298},"All input files must be uploaded onto the DNAnexus platform.\nWhen specifying files for input you can use either the DNAnexus fie IDs (e.g. ",{"type":431,"tag":668,"props":1300,"children":1302},{"className":1301},[],[1303],{"type":476,"value":1304},"file-FBgvp680gz1bGQ5p8yZKz69g",{"type":476,"value":1306},"), or the file names if they are unique.\nFor an idea of how to upload files to DNAnexus, see ",{"type":431,"tag":498,"props":1308,"children":1311},{"href":1309,"rel":1310},"https://documentation.dnanexus.com/user/objects/uploading-and-downloading-files/small-sets-of-files/uploading-using-dx#uploading-files",[502],[1312],{"type":476,"value":1313},"this guide",{"type":476,"value":675},{"type":431,"tag":619,"props":1316,"children":1318},{"id":1317},"step-1-running-vep",[1319],{"type":476,"value":1320},"Step 1: Running VEP+",{"type":431,"tag":432,"props":1322,"children":1323},{},[1324,1326,1331],{"type":476,"value":1325},"To run the VEP+ DNAnexus app, you can use the following ",{"type":431,"tag":668,"props":1327,"children":1329},{"className":1328},[],[1330],{"type":476,"value":1252},{"type":476,"value":1332}," command with your own inputs in place of the example's:",{"type":431,"tag":1334,"props":1335,"children":1339},"pre",{"className":1336,"code":1337,"language":1338,"meta":424,"style":424},"language-bash shiki shiki-themes material-theme-lighter material-theme material-theme-palenight","dx run app-stjude_vep_plus -iinput_file=my_vcf.vcf -igenome_string=GRCh37-lite 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