{"id":20769295,"url":"https://github.com/bioinfo-chru-strasbourg/howard","last_synced_at":"2025-04-30T12:13:00.286Z","repository":{"id":110334680,"uuid":"169592472","full_name":"bioinfo-chru-strasbourg/howard","owner":"bioinfo-chru-strasbourg","description":"Highly Open Workflow for Annotation \u0026 Ranking toward genomic variant Discovery","archived":false,"fork":false,"pushed_at":"2024-10-24T12:56:02.000Z","size":126270,"stargazers_count":6,"open_issues_count":14,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-10-25T14:07:41.532Z","etag":null,"topics":["annotation","annovar","duckdb","genetic","parquet","prioritization","snpeff","variations","vcf"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bioinfo-chru-strasbourg.png","metadata":{"files":{"readme":"README.html","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-02-07T15:19:54.000Z","updated_at":"2024-09-11T12:47:05.000Z","dependencies_parsed_at":null,"dependency_job_id":"ccbabbe3-8bd6-491a-b139-039defd22d6e","html_url":"https://github.com/bioinfo-chru-strasbourg/howard","commit_stats":{"total_commits":70,"total_committers":1,"mean_commits":70.0,"dds":0.0,"last_synced_commit":"c9b98a8b37e80759321e3137468eea18503e619a"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinfo-chru-strasbourg%2Fhoward","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinfo-chru-strasbourg%2Fhoward/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinfo-chru-strasbourg%2Fhoward/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinfo-chru-strasbourg%2Fhoward/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bioinfo-chru-strasbourg","download_url":"https://codeload.github.com/bioinfo-chru-strasbourg/howard/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225033739,"owners_count":17410513,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["annotation","annovar","duckdb","genetic","parquet","prioritization","snpeff","variations","vcf"],"created_at":"2024-11-17T11:43:13.336Z","updated_at":"2025-04-30T12:13:00.275Z","avatar_url":"https://github.com/bioinfo-chru-strasbourg.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!DOCTYPE html\u003e\n\u003chtml xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"\" xml:lang=\"\"\u003e\n\u003chead\u003e\n \u003cmeta charset=\"utf-8\" /\u003e\n \u003cmeta name=\"generator\" content=\"pandoc\" /\u003e\n \u003cmeta name=\"viewport\" content=\"width=device-width, initial-scale=1.0, user-scalable=yes\" /\u003e\n \u003ctitle\u003eHOWARD README\u003c/title\u003e\n \u003cstyle\u003e\n html {\n color: #1a1a1a;\n background-color: #fdfdfd;\n }\n body {\n margin: 0 auto;\n max-width: 1000px;\n padding-left: 50px;\n padding-right: 50px;\n padding-top: 50px;\n padding-bottom: 50px;\n hyphens: auto;\n overflow-wrap: break-word;\n text-rendering: optimizeLegibility;\n font-kerning: normal;\n }\n @media (max-width: 600px) {\n body {\n font-size: 0.9em;\n padding: 12px;\n }\n h1 {\n font-size: 1.8em;\n }\n }\n @media print {\n html {\n background-color: white;\n }\n body {\n background-color: transparent;\n color: black;\n font-size: 12pt;\n }\n p, h2, h3 {\n orphans: 3;\n widows: 3;\n }\n h2, h3, h4 {\n page-break-after: avoid;\n }\n }\n p {\n margin: 1em 0;\n }\n a {\n color: #1a1a1a;\n }\n a:visited {\n color: #1a1a1a;\n }\n img {\n max-width: 100%;\n }\n svg {\n height: auto;\n max-width: 100%;\n }\n h1, h2, h3, h4, h5, h6 {\n margin-top: 1.4em;\n }\n h5, h6 {\n font-size: 1em;\n font-style: italic;\n }\n h6 {\n font-weight: normal;\n }\n ol, ul {\n padding-left: 1.7em;\n margin-top: 1em;\n }\n li \u003e ol, li \u003e ul {\n margin-top: 0;\n }\n blockquote {\n margin: 1em 0 1em 1.7em;\n padding-left: 1em;\n border-left: 2px solid #e6e6e6;\n color: #606060;\n }\n code {\n font-family: Menlo, Monaco, Consolas, 'Lucida Console', monospace;\n font-size: 85%;\n margin: 0;\n hyphens: manual;\n }\n pre {\n margin: 1em 0;\n overflow: auto;\n }\n pre code {\n padding: 0;\n overflow: visible;\n overflow-wrap: normal;\n }\n .sourceCode {\n background-color: transparent;\n overflow: visible;\n }\n hr {\n background-color: #1a1a1a;\n border: none;\n height: 1px;\n margin: 1em 0;\n }\n table {\n margin: 1em 0;\n border-collapse: collapse;\n width: 100%;\n overflow-x: auto;\n display: block;\n font-variant-numeric: lining-nums tabular-nums;\n }\n table caption {\n margin-bottom: 0.75em;\n }\n tbody {\n margin-top: 0.5em;\n border-top: 1px solid #1a1a1a;\n border-bottom: 1px solid #1a1a1a;\n }\n th {\n border-top: 1px solid #1a1a1a;\n padding: 0.25em 0.5em 0.25em 0.5em;\n }\n td {\n padding: 0.125em 0.5em 0.25em 0.5em;\n }\n header {\n margin-bottom: 4em;\n text-align: center;\n }\n #TOC li {\n list-style: none;\n }\n #TOC ul {\n padding-left: 1.3em;\n }\n #TOC \u003e ul {\n padding-left: 0;\n }\n #TOC a:not(:hover) {\n text-decoration: none;\n }\n code{white-space: pre-wrap;}\n span.smallcaps{font-variant: small-caps;}\n div.columns{display: flex; gap: min(4vw, 1.5em);}\n div.column{flex: auto; overflow-x: auto;}\n div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}\n /* The extra [class] is a hack that increases specificity enough to\n override a similar rule in reveal.js */\n ul.task-list[class]{list-style: none;}\n ul.task-list li input[type=\"checkbox\"] {\n font-size: inherit;\n width: 0.8em;\n margin: 0 0.8em 0.2em -1.6em;\n vertical-align: middle;\n }\n .display.math{display: block; text-align: center; margin: 0.5rem auto;}\n /* CSS for syntax highlighting */\n pre \u003e code.sourceCode { white-space: pre; position: relative; }\n pre \u003e code.sourceCode \u003e span { line-height: 1.25; }\n pre \u003e code.sourceCode \u003e span:empty { height: 1.2em; }\n .sourceCode { overflow: visible; }\n code.sourceCode \u003e span { color: inherit; text-decoration: inherit; }\n div.sourceCode { margin: 1em 0; }\n pre.sourceCode { margin: 0; }\n @media screen {\n div.sourceCode { overflow: auto; }\n }\n @media print {\n pre \u003e code.sourceCode { white-space: pre-wrap; }\n pre \u003e code.sourceCode \u003e span { display: inline-block; text-indent: -5em; padding-left: 5em; }\n }\n pre.numberSource code\n { counter-reset: source-line 0; }\n pre.numberSource code \u003e span\n { position: relative; left: -4em; counter-increment: source-line; }\n pre.numberSource code \u003e span \u003e a:first-child::before\n { content: counter(source-line);\n position: relative; left: -1em; text-align: right; vertical-align: baseline;\n border: none; display: inline-block;\n -webkit-touch-callout: none; -webkit-user-select: none;\n -khtml-user-select: none; -moz-user-select: none;\n -ms-user-select: none; user-select: none;\n padding: 0 4px; width: 4em;\n color: #aaaaaa;\n }\n pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }\n div.sourceCode\n { }\n @media screen {\n pre \u003e code.sourceCode \u003e span \u003e a:first-child::before { text-decoration: underline; }\n }\n code span.al { color: #ff0000; font-weight: bold; } /* Alert */\n code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */\n code span.at { color: #7d9029; } /* Attribute */\n code span.bn { color: #40a070; } /* BaseN */\n code span.bu { color: #008000; } /* BuiltIn */\n code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */\n code span.ch { color: #4070a0; } /* Char */\n code span.cn { color: #880000; } /* Constant */\n code span.co { color: #60a0b0; font-style: italic; } /* Comment */\n code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */\n code span.do { color: #ba2121; font-style: italic; } /* Documentation */\n code span.dt { color: #902000; } /* DataType */\n code span.dv { color: #40a070; } /* DecVal */\n code span.er { color: #ff0000; font-weight: bold; } /* Error */\n code span.ex { } /* Extension */\n code span.fl { color: #40a070; } /* Float */\n code span.fu { color: #06287e; } /* Function */\n code span.im { color: #008000; font-weight: bold; } /* Import */\n code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */\n code span.kw { color: #007020; font-weight: bold; } /* Keyword */\n code span.op { color: #666666; } /* Operator */\n code span.ot { color: #007020; } /* Other */\n code span.pp { color: #bc7a00; } /* Preprocessor */\n code span.sc { color: #4070a0; } /* SpecialChar */\n code span.ss { color: #bb6688; } /* SpecialString */\n code span.st { color: #4070a0; } /* String */\n code span.va { color: #19177c; } /* Variable */\n code span.vs { color: #4070a0; } /* VerbatimString */\n code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */\n \u003c/style\u003e\n\u003c/head\u003e\n\u003cbody\u003e\n\u003cheader id=\"title-block-header\"\u003e\n\u003ch1 class=\"title\"\u003eHOWARD README\u003c/h1\u003e\n\u003c/header\u003e\n\u003ch1 data-number=\"1\" id=\"howard\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e1\u003c/span\u003e HOWARD\u003c/h1\u003e\n\u003cfigure\u003e\n\u003cimg src=\"images/icon.png\" title=\"HOWARD - Highly Open Workflow for Annotation \u0026 Ranking toward genomic variant\nDiscovery\"\nalt=\"HOWARD - Highly Open Workflow for Annotation \u0026 Ranking toward genomic variant\nDiscovery\" /\u003e\n\u003cfigcaption aria-hidden=\"true\"\u003e\nHOWARD - Highly Open Workflow for Annotation \u0026amp; Ranking toward\ngenomic variant Discovery\n\u003c/figcaption\u003e\n\u003c/figure\u003e\n\u003cp\u003eHighly Open Workflow for Annotation \u0026amp; Ranking toward genomic\nvariant Discovery\u003c/p\u003e\n\u003cp\u003eHOWARD annotates and prioritizes genetic variations, calculates and\nnormalizes annotations, translates files in multiple formats (e.g.\u0026#xA0;vcf,\ntsv, parquet) and generates variants statistics.\u003c/p\u003e\n\u003cp\u003eHOWARD annotation is mainly based on a build-in Parquet annotation\nmethod, and external tools such as BCFTOOLS, ANNOVAR, snpEff, Exomiser\nand Splice (see docs, automatically downloaded if needed). Parquet\nannotation uses annotation database in VCF or BED format, in mutliple\nfile format: Parquet/duckdb, VCF, BED, TSV, CSV, TBL, JSON.\u003c/p\u003e\n\u003cp\u003eHOWARD calculation processes variants information to calculate new\ninformation, such as: harmonizes allele frequency (VAF), extracts Nomen\n(transcript, cNomen, pNomen\u0026#x2026;) from HGVS fields with an optional list of\npersonalized transcripts, generates VaRank format barcode.\u003c/p\u003e\n\u003cp\u003eHOWARD prioritization algorithm uses profiles to flag variants (as\npassed or filtered), calculate a prioritization score, and automatically\ngenerate a comment for each variants (example: \u0026#x2018;polymorphism identified\nin dbSNP. associated to Lung Cancer. Found in ClinVar\ndatabase\u0026#x2019;).Prioritization profiles are defined in a configuration file.\nA profile is defined as a list of annotation/value, using wildcards and\ncomparison options (contains, lower than, greater than, equal\u0026#x2026;).\nAnnotations fields may be quality values (usually from callers, such as\n\u0026#x2018;GQ\u0026#x2019;, \u0026#x2018;DP\u0026#x2019;) or other annotations fields provided by annotations tools,\nsuch as HOWARD itself (example: COSMIC, Clinvar, 1000genomes, PolyPhen,\nSIFT). Multiple profiles can be used simultaneously, which is useful to\ndefine multiple validation/prioritization levels (example: \u0026#x2018;standard\u0026#x2019;,\n\u0026#x2018;stringent\u0026#x2019;, \u0026#x2018;rare variants\u0026#x2019;, \u0026#x2018;low allele frequency\u0026#x2019;).\u003c/p\u003e\n\u003cp\u003eHOWARD translates VCF format into multiple formats (e.g.\u0026#xA0;VCF, TSV,\nParquet), by sorting variants using specific fields (example :\n\u0026#x2018;prioritization score\u0026#x2019;, \u0026#x2018;allele frequency\u0026#x2019;, \u0026#x2018;gene symbol\u0026#x2019;),\nincluding/excluding annotations/fields, including/excluding variants,\nadding fixed columns.\u003c/p\u003e\n\u003cp\u003eHOWARD generates statistics files with a specific algorithm, snpEff\nand BCFTOOLS.\u003c/p\u003e\n\u003cp\u003eHOWARD is multithreaded through the number of variants and by\ndatabase (data-scaling).\u003c/p\u003e\n\u003cp\u003eHOWARD is able to add plugins for further analyses.\u003c/p\u003e\n\u003ch2 data-number=\"1.1\" id=\"table-of-contents\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e1.1\u003c/span\u003e Table of contents\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"#installation\"\u003eInstallation\u003c/a\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"#download\"\u003eDownload\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#python\"\u003ePython\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#docker\"\u003eDocker\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#databases\"\u003eDatabases\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#configuration\"\u003eConfiguration\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#tools\"\u003eTools\u003c/a\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"#parameters\"\u003eParameters\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#stats\"\u003eStats\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#convert\"\u003eConvert\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#query\"\u003eQuery\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#annotation\"\u003eAnnotation\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#calculation\"\u003eCalculation\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#prioritization\"\u003ePrioritization\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#hgvs-annotation\"\u003eHGVS annotation\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#process\"\u003eProcess\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#documentation\"\u003eDocumentation\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#contact\"\u003eContact\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch1 data-number=\"2\" id=\"installation\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e2\u003c/span\u003e Installation\u003c/h1\u003e\n\u003cp\u003eHOWARD can be installed using \u003ca href=\"#python\"\u003ePython\u003c/a\u003e, and a \u003ca\nhref=\"#docker\"\u003eDocker\u003c/a\u003e installation provides a CLI (Command Line\nInterface) with all external tools and useful databases. \u003ca\nhref=\"#databases\"\u003eDatabases\u003c/a\u003e can be automatically downloaded, or\nhome-made generated (created or downloaded).\u003c/p\u003e\n\u003ch2 data-number=\"2.1\" id=\"download\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e2.1\u003c/span\u003e Download\u003c/h2\u003e\n\u003cp\u003eDownload sources from gitHub\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb1\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb1-1\"\u003e\u003ca href=\"#cb1-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"fu\"\u003emkdir\u003c/span\u003e \u003cspan class=\"at\"\u003e-p\u003c/span\u003e ~/howard/src\u003c/span\u003e\n\u003cspan id=\"cb1-2\"\u003e\u003ca href=\"#cb1-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"bu\"\u003ecd\u003c/span\u003e ~/howard/src\u003c/span\u003e\n\u003cspan id=\"cb1-3\"\u003e\u003ca href=\"#cb1-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"fu\"\u003egit\u003c/span\u003e clone https://github.com/bioinfo-chru-strasbourg/howard.git .\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003ch2 data-number=\"2.2\" id=\"python\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e2.2\u003c/span\u003e Python\u003c/h2\u003e\n\u003cp\u003eInstall HOWARD using Python Pip tool, and run HOWARD for help\noptions:\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb2\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb2-1\"\u003e\u003ca href=\"#cb2-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003econda\u003c/span\u003e create \u003cspan class=\"at\"\u003e--name\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003ehoward python=3.10\u003c/span\u003e\n\u003cspan id=\"cb2-2\"\u003e\u003ca href=\"#cb2-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003econda\u003c/span\u003e activate howard\u003c/span\u003e\n\u003cspan id=\"cb2-3\"\u003e\u003ca href=\"#cb2-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003epython\u003c/span\u003e \u003cspan class=\"at\"\u003e-m\u003c/span\u003e pip install \u003cspan class=\"at\"\u003e-e\u003c/span\u003e .\u003c/span\u003e\n\u003cspan id=\"cb2-4\"\u003e\u003ca href=\"#cb2-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e \u003cspan class=\"at\"\u003e--help\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cpre class=\"text\"\u003e\u003ccode\u003eusage: howard [-h] {query,stats,convert,hgvs,annotation,calculation,prioritization,process,databases,gui} ...\n\nHOWARD:0.12.1.1 - Highly Open Workflow for Annotation \u0026amp; Ranking toward genomic variant Discovery\n\nShared arguments:\n -h, --help show this help message and exit\n\nTools:\n {query,stats,convert,hgvs,annotation,calculation,prioritization,process,databases,gui}\n query Query genetic variations file in SQL format.\n stats Statistics on genetic variations file.\n convert Convert genetic variations file to another format.\n hgvs HGVS annotation (HUGO internation nomenclature) using refGene,\n genome and transcripts list.\n annotation Annotation of genetic variations file using databases/files and tools.\n calculation Calculation operations on genetic variations file and genotype information.\n prioritization Prioritization of genetic variations based on annotations criteria (profiles).\n process Full genetic variations process: annotation, calculation, prioritization, \n format, query, filter...\n databases Download databases and needed files for howard and associated tools\n gui Graphical User Interface tools\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eInstall HOWARD Graphical User Interface using Python Pip tool with\nsupplementary packages, and run as a tool:\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb4\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb4-1\"\u003e\u003ca href=\"#cb4-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003epython\u003c/span\u003e \u003cspan class=\"at\"\u003e-m\u003c/span\u003e pip install \u003cspan class=\"at\"\u003e-r\u003c/span\u003e requirements-gui.txt\u003c/span\u003e\n\u003cspan id=\"cb4-2\"\u003e\u003ca href=\"#cb4-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e gui\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cfigure\u003e\n\u003cimg src=\"images/howard-gui.png\" title=\"HOWARD Graphical User Interface\"\nalt=\"HOWARD Graphical User Interface\" /\u003e\n\u003cfigcaption aria-hidden=\"true\"\u003e\nHOWARD Graphical User Interface\n\u003c/figcaption\u003e\n\u003c/figure\u003e\n\u003ch2 data-number=\"2.3\" id=\"docker\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e2.3\u003c/span\u003e Docker\u003c/h2\u003e\n\u003cp\u003eIn order to build, setup and create a persitent CLI (running\ncontainer with all useful external tools such as \u003ca\nhref=\"https://samtools.github.io/bcftools/\"\u003eBCFTools\u003c/a\u003e, \u003ca\nhref=\"https://pcingola.github.io/SnpEff/\"\u003esnpEff\u003c/a\u003e, \u003ca\nhref=\"https://annovar.openbioinformatics.org/\"\u003eAnnovar\u003c/a\u003e, \u003ca\nhref=\"https://www.sanger.ac.uk/tool/exomiser/\"\u003eExomiser\u003c/a\u003e),\ndocker-compose command build images and launch services as\ncontainers.\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb5\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb5-1\"\u003e\u003ca href=\"#cb5-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003edocker-compose\u003c/span\u003e up \u003cspan class=\"at\"\u003e-d\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eA setup container (HOWARD-setup) will download useful databases (take\na while). To avoid databases download (see \u003ca\nhref=\"#databases\"\u003eDatabases section\u003c/a\u003e to download manually), just\nstart:\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb6\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb6-1\"\u003e\u003ca href=\"#cb6-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003edocker-compose\u003c/span\u003e up \u003cspan class=\"at\"\u003e-d\u003c/span\u003e HOWARD-CLI\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eA Command Line Interface container (HOWARD-CLI) is started with host\ndata and databases folders mounted (by default in ~/howard folder, i.e.\n\u003ccode\u003e~/howard/data:/data\u003c/code\u003e and\n\u003ccode\u003e~/howard/databases:/databases\u003c/code\u003e). Let\u0026#x2019;s play within Docker\nHOWARD-CLI service!\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb7\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb7-1\"\u003e\u003ca href=\"#cb7-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003edocker\u003c/span\u003e exec \u003cspan class=\"at\"\u003e-ti\u003c/span\u003e HOWARD-CLI bash\u003c/span\u003e\n\u003cspan id=\"cb7-2\"\u003e\u003ca href=\"#cb7-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e \u003cspan class=\"at\"\u003e--help\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cp\u003eDocker HOWARD-CLI container (Command Line Interface) can be used to\nexecute commands.\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Query of an existing VCF\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb8\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb8-1\"\u003e\u003ca href=\"#cb8-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003edocker\u003c/span\u003e exec HOWARD-CLI \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb8-2\"\u003e\u003ca href=\"#cb8-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e howard query \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb8-3\"\u003e\u003ca href=\"#cb8-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tool/tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb8-4\"\u003e\u003ca href=\"#cb8-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--query\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;SELECT * FROM variants\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: VCF annotation using HOWARD-CLI (snpEff and ANNOVAR\ndatabases will be automatically downloaded), and query list of genes\nwith HGVS\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb9\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb9-1\"\u003e\u003ca href=\"#cb9-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003edocker\u003c/span\u003e exec \u003cspan class=\"at\"\u003e--workdir\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e/tool HOWARD-CLI \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-2\"\u003e\u003ca href=\"#cb9-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e howard process \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-3\"\u003e\u003ca href=\"#cb9-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--config\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;config/config.json\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-4\"\u003e\u003ca href=\"#cb9-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--param\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;config/param.json\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-5\"\u003e\u003ca href=\"#cb9-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-6\"\u003e\u003ca href=\"#cb9-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.process.tsv\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-7\"\u003e\u003ca href=\"#cb9-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--explode_infos\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-8\"\u003e\u003ca href=\"#cb9-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--query\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026quot;SELECT NOMEN, PZFlag, PZScore, PZComment \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-9\"\u003e\u003ca href=\"#cb9-9\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e FROM variants \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb9-10\"\u003e\u003ca href=\"#cb9-10\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e ORDER BY PZScore DESC\u0026quot;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"2.4\" id=\"databases\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e2.4\u003c/span\u003e Databases\u003c/h2\u003e\n\u003cp\u003eMultiple databases can be automatically downloaded with databases\ntool, such as:\u003c/p\u003e\n\u003ctable\u003e\n\u003ccolgroup\u003e\n\u003ccol style=\"width: 20%\" /\u003e\n\u003ccol style=\"width: 80%\" /\u003e\n\u003c/colgroup\u003e\n\u003cthead\u003e\n\u003ctr\u003e\n\u003cth\u003edatabase\u003c/th\u003e\n\u003cth\u003edescription\u003c/th\u003e\n\u003c/tr\u003e\n\u003c/thead\u003e\n\u003ctbody\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"https://genome.ucsc.edu/cgi-bin/hgGateway\"\u003eGenome\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eGenome Reference Consortium Human\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca\nhref=\"https://annovar.openbioinformatics.org/en/latest/\"\u003eAnnovar\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eANNOVAR is an efficient software tool to utilize update-to-date\ninformation to functionally annotate genetic variants detected from\ndiverse genomes\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"https://pcingola.github.io/SnpEff/\"\u003esnpEff\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eGenetic variant annotation, and functional effect prediction\ntoolbox\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"https://www.ncbi.nlm.nih.gov/refseq/\"\u003erefSeq\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eA comprehensive, integrated, non-redundant, well-annotated set of\nreference sequences including genomic, transcript, and protein\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"https://www.ncbi.nlm.nih.gov/snp/\"\u003edbSNP\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003edbSNP contains human single nucleotide variations, microsatellites,\nand small-scale insertions and deletions along with publication,\npopulation frequency, molecular consequence, and genomic and RefSeq\nmapping information for both common variations and clinical\nmutations\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca\nhref=\"https://sites.google.com/site/jpopgen/dbNSFP\"\u003edbNSFP\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003edbNSFP is a database developed for functional prediction and\nannotation of all potential non-synonymous single-nucleotide variants\n(nsSNVs) in the human genome\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca\nhref=\"https://github.com/google-deepmind/alphamissense\"\u003eAlphaMissense\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eAlphaMissense model implementation\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"https://www.sanger.ac.uk/tool/exomiser/\"\u003eExomiser\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eThe Exomiser is a Java program that finds potential disease-causing\nvariants from whole-exome or whole-genome sequencing data\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Download Multiple databases in the same time for assembly\n\u0026#x2018;hg19\u0026#x2019; (can take a while)\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb10\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb10-1\"\u003e\u003ca href=\"#cb10-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e databases \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-2\"\u003e\u003ca href=\"#cb10-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--assembly\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003ehg19 \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-3\"\u003e\u003ca href=\"#cb10-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-genomes\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/genomes/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-4\"\u003e\u003ca href=\"#cb10-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-genomes-provider\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;UCSC\u0026#39;\u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-5\"\u003e\u003ca href=\"#cb10-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-genomes-contig-regex\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;chr[0-9XYM]+$\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-6\"\u003e\u003ca href=\"#cb10-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-annovar\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/annovar/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-7\"\u003e\u003ca href=\"#cb10-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-annovar-files\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;refGene,cosmic70,nci60\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-8\"\u003e\u003ca href=\"#cb10-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-snpeff\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/snpeff/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-9\"\u003e\u003ca href=\"#cb10-9\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-refseq\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/refseq/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-10\"\u003e\u003ca href=\"#cb10-10\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-refseq-format-file\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;ncbiRefSeq.txt\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-11\"\u003e\u003ca href=\"#cb10-11\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-dbnsfp\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/dbnsfp/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-12\"\u003e\u003ca href=\"#cb10-12\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-dbnsfp-release\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;4.4a\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-13\"\u003e\u003ca href=\"#cb10-13\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-dbnsfp-subdatabases\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-14\"\u003e\u003ca href=\"#cb10-14\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-alphamissense\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/alphamissense/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-15\"\u003e\u003ca href=\"#cb10-15\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-exomiser\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/exomiser/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-16\"\u003e\u003ca href=\"#cb10-16\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-dbsnp\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;~/howard/databases/dbsnp/current\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-17\"\u003e\u003ca href=\"#cb10-17\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--download-dbsnp-vcf\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb10-18\"\u003e\u003ca href=\"#cb10-18\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--threads\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e8\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#databases-tool\"\u003eHOWARD Help Databases\ntool\u003c/a\u003e for more information.\u003c/p\u003e\n\u003cp\u003eDatabases can be home-made generated, starting with a existing\nannotation file, especially using \u003ca href=\"#convert\"\u003eHOWARD convert\u003c/a\u003e\ntool. These files need to contain specific fields (depending on the\nannotation type):\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003evariant annotation: \u0026#x2018;#CHROM\u0026#x2019;, \u0026#x2018;POS\u0026#x2019;, \u0026#x2018;ALT\u0026#x2019;, \u0026#x2018;REF\u0026#x2019;\u003c/li\u003e\n\u003cli\u003eregion annotation: \u0026#x2018;#CHROM\u0026#x2019;, \u0026#x2018;START\u0026#x2019;, \u0026#x2018;STOP\u0026#x2019;\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eEach database annotation file is associated with a \u0026#x2018;header\u0026#x2019; file\n(\u0026#x2018;.hdr\u0026#x2019;), in VCF header format, to describe annotations within the\ndatabase.\u003c/p\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"2.5\" id=\"configuration\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e2.5\u003c/span\u003e Configuration\u003c/h2\u003e\n\u003cp\u003eHOWARD Configuration JSON file defined default configuration\nregarding resources (e.g.\u0026#xA0;threads, memory), settings (e.g.\u0026#xA0;verbosity,\ntemporary files), default folders (e.g.\u0026#xA0;for databases) and paths to\nexternal tools.\u003c/p\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.config.html\"\u003eHOWARD Configuration JSON\u003c/a\u003e for\nmore information.\u003c/p\u003e\n\u003ch1 data-number=\"3\" id=\"tools\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3\u003c/span\u003e Tools\u003c/h1\u003e\n\u003cp\u003eHOWARD annotates and prioritizes genetic variations, calculates and\nnormalizes annotations, convert on multiple formats, query variations\nand generates statistics. These tools require options or a \u003ca\nhref=\"help.param.html\"\u003eParameters JSON\u003c/a\u003e file.\u003c/p\u003e\n\u003ch2 data-number=\"3.1\" id=\"parameters\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.1\u003c/span\u003e Parameters\u003c/h2\u003e\n\u003cp\u003eHOWARD Parameters JSON file defined parameters to process\nannotations, prioritization, calculations, convertions and queries. Use\nthis parameters file to configure tools, instead of options or as a main\nconfiguration (options will replace parameters in JSON file).\u003c/p\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.param.html\"\u003eHOWARD Parameters JSON\u003c/a\u003e for\nmore information.\u003c/p\u003e\n\u003ch2 data-number=\"3.2\" id=\"stats\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.2\u003c/span\u003e Stats\u003c/h2\u003e\n\u003cp\u003eStatistics on genetic variations, such as: number of variants, number\nof samples, statistics by chromosome, genotypes by samples, annotations.\nTheses statsitics can be applied to VCF files and all database\nannotation files.\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Show example VCF statistics and brief overview\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb11\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb11-1\"\u003e\u003ca href=\"#cb11-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e stats \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb11-2\"\u003e\u003ca href=\"#cb11-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#stats-tool\"\u003eHOWARD Help Stats tool\u003c/a\u003e\nfor more information.\u003c/p\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"3.3\" id=\"convert\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.3\u003c/span\u003e Convert\u003c/h2\u003e\n\u003cp\u003eConvert genetic variations file to another format. Multiple format\nare available, such as usual and official VCF format, but also other\nformats such as TSV, CSV, TBL, JSON and Parquet/duckDB. These formats\nneed a header \u0026#x2018;.hdr\u0026#x2019; file to take advantage of the power of howard\n(especially through INFO/tag definition), and using howard convert tool\nautomatically generate header file fo futher use (otherwise, an default\n\u0026#x2018;.hdr\u0026#x2019; file is generated).\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Translate VCF into TSV, export INFO/tags into columns, and\nshow output file\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb12\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb12-1\"\u003e\u003ca href=\"#cb12-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e convert \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb12-2\"\u003e\u003ca href=\"#cb12-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb12-3\"\u003e\u003ca href=\"#cb12-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--explode_infos\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb12-4\"\u003e\u003ca href=\"#cb12-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.tsv\u0026#39;\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb12-5\"\u003e\u003ca href=\"#cb12-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"fu\"\u003ecat\u003c/span\u003e \u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.tsv\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#convert-tool\"\u003eHOWARD Help Convert\ntool\u003c/a\u003e for more options.\u003c/p\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"3.4\" id=\"query\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.4\u003c/span\u003e Query\u003c/h2\u003e\n\u003cp\u003eQuery genetic variations in SQL format. Data can be loaded into\n\u0026#x2018;variants\u0026#x2019; table from various formats (e.g.\u0026#xA0;VCF, TSV, Parquet\u0026#x2026;). Using\n\u0026#x2018;explode\u0026#x2019; option allows querying on INFO/tag annotations. SQL query can\nalso use external data within the request, such as a Parquet\nfile(s).\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Select variants in VCF with INFO Tags criterions\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb13\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb13-1\"\u003e\u003ca href=\"#cb13-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e query \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb13-2\"\u003e\u003ca href=\"#cb13-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb13-3\"\u003e\u003ca href=\"#cb13-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--explode_infos\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb13-4\"\u003e\u003ca href=\"#cb13-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--query\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;SELECT \u0026quot;#CHROM\u0026quot;, POS, REF, ALT, DP, CLNSIG, sample2, sample3 \u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb13-5\"\u003e\u003ca href=\"#cb13-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e FROM variants \u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb13-6\"\u003e\u003ca href=\"#cb13-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e WHERE DP \u0026gt;= 50 OR CLNSIG NOT NULL \u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb13-7\"\u003e\u003ca href=\"#cb13-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e ORDER BY CLNSIG DESC, DP DESC\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#query-tool\"\u003eHOWARD Help Query tool\u003c/a\u003e\nfor more options.\u003c/p\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"3.5\" id=\"annotation\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.5\u003c/span\u003e Annotation\u003c/h2\u003e\n\u003cp\u003eAnnotation is mainly based on a build-in Parquet annotation method,\nusing database format such as Parquet, duckdb, VCF, BED, TSV, JSON.\nExternal annotation tools are also available, such as BCFTOOLS, Annovar,\nsnpEff, Exomiser and Splice. It uses available databases and homemade\ndatabases. Annovar and snpEff databases are automatically downloaded\n(see \u003ca href=\"docs/help.html#databases-tool\"\u003eHOWARD Help Databases\ntool\u003c/a\u003e). All annotation parameters are defined in \u003ca\nhref=\"docs/help.param.html\"\u003eHOWARD Parameters JSON\u003c/a\u003e file.\u003c/p\u003e\n\u003cp\u003eQuick annotation allows to annotates by simply listing annotation\ndatabases, or defining external tools keywords. These annotations can be\ncombined.\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: VCF annotation with Parquet and VCF databases, output as VCF\nformat\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb14\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb14-1\"\u003e\u003ca href=\"#cb14-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e annotation \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb14-2\"\u003e\u003ca href=\"#cb14-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb14-3\"\u003e\u003ca href=\"#cb14-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--annotations\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/databases/annotations/current/hg19/dbnsfp42a.parquet,\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb14-4\"\u003e\u003ca href=\"#cb14-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e tests/databases/annotations/current/hg19/cosmic70.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb14-5\"\u003e\u003ca href=\"#cb14-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.howard.vcf.gz\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: VCF annotation with external tools (Annovar refGene and\nsnpEff databases), output as TSV format\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb15\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb15-1\"\u003e\u003ca href=\"#cb15-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e annotation \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb15-2\"\u003e\u003ca href=\"#cb15-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb15-3\"\u003e\u003ca href=\"#cb15-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--annotations\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;annovar:refGene,snpeff\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb15-4\"\u003e\u003ca href=\"#cb15-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.howard.tsv\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#annotation-tool\"\u003eHOWARD Help Annotation\ntool\u003c/a\u003e for more options.\u003c/p\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"3.6\" id=\"calculation\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.6\u003c/span\u003e Calculation\u003c/h2\u003e\n\u003cp\u003eCalculation processes variants information to generate new\ninformation, such as: identify variation type (VarType), harmonizes\nallele frequency (VAF) and calculate sttistics (VAF_stats), extracts\nNomen (transcript, cNomen, pNomen\u0026#x2026;) from an HGVS field (e.g.\u0026#xA0;snpEff,\nAnnovar) with an optional list of personalized transcripts, generates\nVaRank format barcode, identify trio inheritance.\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Identify variant types and generate a table of variant type\ncount\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb16\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb16-1\"\u003e\u003ca href=\"#cb16-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e calculation \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-2\"\u003e\u003ca href=\"#cb16-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.full.vcf\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-3\"\u003e\u003ca href=\"#cb16-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--calculations\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;vartype\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-4\"\u003e\u003ca href=\"#cb16-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.calculation.tsv\u0026#39;\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-5\"\u003e\u003ca href=\"#cb16-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-6\"\u003e\u003ca href=\"#cb16-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e query \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-7\"\u003e\u003ca href=\"#cb16-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.calculation.tsv\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-8\"\u003e\u003ca href=\"#cb16-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--explode_infos\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-9\"\u003e\u003ca href=\"#cb16-9\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--query\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;SELECT\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-10\"\u003e\u003ca href=\"#cb16-10\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e \u0026quot;VARTYPE\u0026quot; AS \u0026#39;\u003c/span\u003eVariantType\u003cspan class=\"st\"\u003e\u0026#39;,\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-11\"\u003e\u003ca href=\"#cb16-11\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e count(*) AS \u0026#39;\u003c/span\u003eCount\u003cspan class=\"st\"\u003e\u0026#39;\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-12\"\u003e\u003ca href=\"#cb16-12\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e FROM variants\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-13\"\u003e\u003ca href=\"#cb16-13\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e GROUP BY \u0026quot;VARTYPE\u0026quot;\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb16-14\"\u003e\u003ca href=\"#cb16-14\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e ORDER BY count DESC\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb17\"\u003e\u003cpre\nclass=\"sourceCode ts\"\u003e\u003ccode class=\"sourceCode typescript\"\u003e\u003cspan id=\"cb17-1\"\u003e\u003ca href=\"#cb17-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e VariantType Count\u003c/span\u003e\n\u003cspan id=\"cb17-2\"\u003e\u003ca href=\"#cb17-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e0\u003c/span\u003e BND \u003cspan class=\"dv\"\u003e7\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-3\"\u003e\u003ca href=\"#cb17-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e DUP \u003cspan class=\"dv\"\u003e6\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-4\"\u003e\u003ca href=\"#cb17-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e2\u003c/span\u003e INS \u003cspan class=\"dv\"\u003e5\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-5\"\u003e\u003ca href=\"#cb17-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e3\u003c/span\u003e SNV \u003cspan class=\"dv\"\u003e4\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-6\"\u003e\u003ca href=\"#cb17-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e4\u003c/span\u003e CNV \u003cspan class=\"dv\"\u003e3\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-7\"\u003e\u003ca href=\"#cb17-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e5\u003c/span\u003e DEL \u003cspan class=\"dv\"\u003e3\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-8\"\u003e\u003ca href=\"#cb17-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e6\u003c/span\u003e INV \u003cspan class=\"dv\"\u003e3\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-9\"\u003e\u003ca href=\"#cb17-9\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e7\u003c/span\u003e MOSAIC \u003cspan class=\"dv\"\u003e2\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-10\"\u003e\u003ca href=\"#cb17-10\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e8\u003c/span\u003e INDEL \u003cspan class=\"dv\"\u003e2\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb17-11\"\u003e\u003ca href=\"#cb17-11\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e9\u003c/span\u003e MNV \u003cspan class=\"dv\"\u003e1\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#calculation-tool\"\u003eHOWARD Help Calculation\ntool\u003c/a\u003e for more options.\u003c/p\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"3.7\" id=\"prioritization\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.7\u003c/span\u003e Prioritization\u003c/h2\u003e\n\u003cp\u003ePrioritization algorithm uses profiles to flag variants (as passed or\nfiltered), calculate a prioritization score, and automatically generate\na comment for each variants (example: \u0026#x2018;polymorphism identified in dbSNP.\nassociated to Lung Cancer. Found in ClinVar database\u0026#x2019;). Prioritization\nprofiles are defined in a configuration file in JSON format. A profile\nis defined as a list of annotation/value, using wildcards and comparison\noptions (contains, lower than, greater than, equal\u0026#x2026;). Annotations fields\nmay be quality values (usually from callers, such as \u0026#x2018;DP\u0026#x2019;) or other\nannotations fields provided by annotations tools, such as HOWARD itself\n(example: COSMIC, Clinvar, 1000genomes, PolyPhen, SIFT).\u003c/p\u003e\n\u003cp\u003eMultiple profiles can be used simultaneously, which is useful to\ndefine multiple validation/prioritization levels (e.g.\u0026#xA0;\u0026#x2018;standard\u0026#x2019;,\n\u0026#x2018;stringent\u0026#x2019;, \u0026#x2018;rare variants\u0026#x2019;). Prioritization score can be calculated\nfollowing multiple mode, either \u0026#x2018;HOWARD\u0026#x2019; (incremental) or \u0026#x2018;VaRank\u0026#x2019;\n(maximum). Prioritization fields can be selected (PZScore, PZFlag,\nPZComment, PZTags, PZInfos).\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Prioritize variants from criteria on INFO annotations for\nprofiles \u0026#x2018;default\u0026#x2019; and \u0026#x2018;GERMLINE\u0026#x2019; (from \u0026#x2018;prioritization_profiles.json\u0026#x2019;\nprofiles configuration), export prioritization tags, and query variants\npassing filters\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb18\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb18-1\"\u003e\u003ca href=\"#cb18-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e prioritization \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb18-2\"\u003e\u003ca href=\"#cb18-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb18-3\"\u003e\u003ca href=\"#cb18-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--prioritization_config\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;config/prioritization_profiles.json\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb18-4\"\u003e\u003ca href=\"#cb18-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--prioritizations\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;default,GERMLINE\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb18-5\"\u003e\u003ca href=\"#cb18-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--default_profile\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;default\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb18-6\"\u003e\u003ca href=\"#cb18-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--pzfields\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;PZFlag,PZScore,PZComment,PZTags,PZInfos\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb18-7\"\u003e\u003ca href=\"#cb18-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--prioritization_score_mode\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;HOWARD\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb18-8\"\u003e\u003ca href=\"#cb18-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.prioritized.vcf.gz\u0026#39;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb19\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb19-1\"\u003e\u003ca href=\"#cb19-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e query \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb19-2\"\u003e\u003ca href=\"#cb19-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.prioritized.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb19-3\"\u003e\u003ca href=\"#cb19-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--explode_infos\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb19-4\"\u003e\u003ca href=\"#cb19-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--query\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026quot;SELECT \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u0026quot;\u003c/span\u003e\u003cspan class=\"st\"\u003e#CHROM\u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u0026quot;\u003c/span\u003e\u003cspan class=\"st\"\u003e, POS, ALT, REF, PZFlag, PZScore, PZTags, DP, CLNSIG \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb19-5\"\u003e\u003ca href=\"#cb19-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e FROM variants \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb19-6\"\u003e\u003ca href=\"#cb19-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e WHERE PZScore \u0026gt; 0 \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb19-7\"\u003e\u003ca href=\"#cb19-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e AND PZFlag == \u0026#39;PASS\u0026#39; \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb19-8\"\u003e\u003ca href=\"#cb19-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e ORDER BY PZScore DESC\u0026quot;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb20\"\u003e\u003cpre\nclass=\"sourceCode ts\"\u003e\u003ccode class=\"sourceCode typescript\"\u003e\u003cspan id=\"cb20-1\"\u003e\u003ca href=\"#cb20-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e #CHROM POS ALT REF PZFlag PZScore PZTags DP CLNSIG\u003c/span\u003e\n\u003cspan id=\"cb20-2\"\u003e\u003ca href=\"#cb20-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e0\u003c/span\u003e chr1 \u003cspan class=\"dv\"\u003e28736\u003c/span\u003e C A PASS \u003cspan class=\"dv\"\u003e15\u003c/span\u003e PZFlag#PASS\u003cspan class=\"op\"\u003e|\u003c/span\u003ePZScore#\u003cspan class=\"fl\"\u003e15.\u003c/span\u003e\u003cspan class=\"op\"\u003e..\u003c/span\u003e \u003cspan class=\"at\"\u003eNaN\u003c/span\u003e pathogenic\u003c/span\u003e\n\u003cspan id=\"cb20-3\"\u003e\u003ca href=\"#cb20-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e chr1 \u003cspan class=\"dv\"\u003e69101\u003c/span\u003e G A PASS \u003cspan class=\"dv\"\u003e5\u003c/span\u003e PZFlag#PASS\u003cspan class=\"op\"\u003e|\u003c/span\u003ePZScore#\u003cspan class=\"dv\"\u003e5\u003c/span\u003e\u003cspan class=\"op\"\u003e|...\u003c/span\u003e \u003cspan class=\"fl\"\u003e50.0\u003c/span\u003e None\u003c/span\u003e\n\u003cspan id=\"cb20-4\"\u003e\u003ca href=\"#cb20-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e2\u003c/span\u003e chr7 \u003cspan class=\"dv\"\u003e55249063\u003c/span\u003e A G PASS \u003cspan class=\"dv\"\u003e5\u003c/span\u003e PZFlag#PASS\u003cspan class=\"op\"\u003e|\u003c/span\u003ePZScore#\u003cspan class=\"dv\"\u003e5\u003c/span\u003e\u003cspan class=\"op\"\u003e|...\u003c/span\u003e \u003cspan class=\"fl\"\u003e125.0\u003c/span\u003e None\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#prioritization-tool\"\u003eHOWARD Help\nPrioritization tool\u003c/a\u003e for more options.\u003c/p\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"3.8\" id=\"hgvs-annotation\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.8\u003c/span\u003e HGVS Annotation\u003c/h2\u003e\n\u003cp\u003eHOWARD annotates variants with HGVS annotation using HUGO HGVS\ninternation Sequence Variant Nomenclature (http://varnomen.hgvs.org/).\nAnnotation refere to refGene and genome to generate HGVS nomenclature\nfor all available transcripts. This annotation add \u0026#x2018;hgvs\u0026#x2019; field into VCF\nINFO column of a VCF file. Several options are available, to add gene,\nexon and protein information, to generate a \u0026#x201C;full format\u0026#x201D; detailed\nannotation, to choose codon format.\u003c/p\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#hgvs-tool\"\u003eHOWARD Help HGVS tool\u003c/a\u003e for\nmore options.\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: HGVS annotation with quick options\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb21\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb21-1\"\u003e\u003ca href=\"#cb21-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e hgvs \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb21-2\"\u003e\u003ca href=\"#cb21-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb21-3\"\u003e\u003ca href=\"#cb21-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.process.tsv\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb21-4\"\u003e\u003ca href=\"#cb21-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--hgvs\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003efull_format,use_exon\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb22\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb22-1\"\u003e\u003ca href=\"#cb22-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e query \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb22-2\"\u003e\u003ca href=\"#cb22-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.process.tsv\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb22-3\"\u003e\u003ca href=\"#cb22-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--explode_infos\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb22-4\"\u003e\u003ca href=\"#cb22-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--query\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026quot;SELECT hgvs \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb22-5\"\u003e\u003ca href=\"#cb22-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e FROM variants \u0026quot;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb23\"\u003e\u003cpre\nclass=\"sourceCode ts\"\u003e\u003ccode class=\"sourceCode typescript\"\u003e\u003cspan id=\"cb23-1\"\u003e\u003ca href=\"#cb23-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e hgvs\u003c/span\u003e\n\u003cspan id=\"cb23-2\"\u003e\u003ca href=\"#cb23-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e0\u003c/span\u003e WASH7P\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_024540\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e50\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e585\u003c/span\u003e\u003cspan class=\"er\"\u003eT\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG\u003c/span\u003e\n\u003cspan id=\"cb23-3\"\u003e\u003ca href=\"#cb23-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e FAM138A\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_026818\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003eexon3\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e597\u003c/span\u003e\u003cspan class=\"er\"\u003eT\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG\u003cspan class=\"op\"\u003e:\u003c/span\u003ep\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"at\"\u003eTyr199Asp\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb23-4\"\u003e\u003ca href=\"#cb23-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e2\u003c/span\u003e OR4F5\u003cspan class=\"op\"\u003e:\u003c/span\u003eNM_001005484\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e2\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003eNP_001005484\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e2\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003eexon3\u003cspan class=\"op\"\u003e:\u003c/span\u003ec\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"fl\"\u003e74.\u003c/span\u003e\u003cspan class=\"op\"\u003e..\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb23-5\"\u003e\u003ca href=\"#cb23-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e3\u003c/span\u003e LINC01128\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_047526\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e287\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e3767\u003c/span\u003e\u003cspan class=\"er\"\u003eA\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG\u003cspan class=\"op\"\u003e,\u003c/span\u003eLINC01128\u003cspan class=\"op\"\u003e:...\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb23-6\"\u003e\u003ca href=\"#cb23-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e4\u003c/span\u003e LINC01128\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_047526\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e287\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e3768\u003c/span\u003e\u003cspan class=\"er\"\u003eA\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG\u003cspan class=\"op\"\u003e,\u003c/span\u003eLINC01128\u003cspan class=\"op\"\u003e:...\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb23-7\"\u003e\u003ca href=\"#cb23-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e5\u003c/span\u003e LINC01128\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_047526\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e287\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e3769\u003c/span\u003e\u003cspan class=\"er\"\u003eA\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG\u003cspan class=\"op\"\u003e,\u003c/span\u003eLINC01128\u003cspan class=\"op\"\u003e:...\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb23-8\"\u003e\u003ca href=\"#cb23-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e6\u003c/span\u003e EGFR\u003cspan class=\"op\"\u003e:\u003c/span\u003eNM_001346897\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e2\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003eNP_001333826\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e\u003cspan class=\"op\"\u003e:\u003c/span\u003eexon19\u003cspan class=\"op\"\u003e:\u003c/span\u003ec\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"fl\"\u003e22.\u003c/span\u003e\u003cspan class=\"op\"\u003e..\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003c/details\u003e\n\u003ch2 data-number=\"3.9\" id=\"process\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e3.9\u003c/span\u003e Process\u003c/h2\u003e\n\u003cp\u003eHOWARD process tool manage genetic variations to:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eannotates genetic variants with multiple annotation databases/files\nand tools\u003c/li\u003e\n\u003cli\u003ecalculates and normalizes annotations\u003c/li\u003e\n\u003cli\u003eprioritizes variants with profiles (list of citeria) to calculate\nscores and flags\u003c/li\u003e\n\u003cli\u003eannotates genetic variants with HGVS nomenclature\u003c/li\u003e\n\u003cli\u003etranslates into various formats\u003c/li\u003e\n\u003cli\u003equery genetic variants and annotations\u003c/li\u003e\n\u003cli\u003egenerates variants statistics\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThis process tool combines all other tools to pipe them in a uniq\ncommand, through available options or a parameters file in JSON format\n(see \u003ca href=\"docs/help.param.html\"\u003eHOWARD Parameters JSON\u003c/a\u003e\nfile).\u003c/p\u003e\n\u003cp\u003eSee \u003ca href=\"docs/help.html#process-tool\"\u003eHOWARD Help Process\ntool\u003c/a\u003e tool for more information.\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003e\nMore details\n\u003c/summary\u003e\n\u003cblockquote\u003e\n\u003cp\u003eExample: Full process command with options (HGVS, annotation,\ncalculation and prioritization)\u003c/p\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb24\"\u003e\u003cpre\nclass=\"sourceCode bash\"\u003e\u003ccode class=\"sourceCode bash\"\u003e\u003cspan id=\"cb24-1\"\u003e\u003ca href=\"#cb24-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"ex\"\u003ehoward\u003c/span\u003e process \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-2\"\u003e\u003ca href=\"#cb24-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--input\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/data/example.vcf.gz\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-3\"\u003e\u003ca href=\"#cb24-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--output\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;/tmp/example.process.tsv\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-4\"\u003e\u003ca href=\"#cb24-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--hgvs\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;full_format,use_exon\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-5\"\u003e\u003ca href=\"#cb24-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--annotations\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;tests/databases/annotations/current/hg19/avsnp150.parquet,\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-6\"\u003e\u003ca href=\"#cb24-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e tests/databases/annotations/current/hg19/dbnsfp42a.parquet,\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-7\"\u003e\u003ca href=\"#cb24-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e tests/databases/annotations/current/hg19/gnomad211_genome.parquet,\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-8\"\u003e\u003ca href=\"#cb24-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e bcftools:tests/databases/annotations/current/hg19/cosmic70.vcf.gz,\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-9\"\u003e\u003ca href=\"#cb24-9\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e snpeff,\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-10\"\u003e\u003ca href=\"#cb24-10\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e annovar:refGene\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-11\"\u003e\u003ca href=\"#cb24-11\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--calculations\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;vartype,snpeff_hgvs,VAF,NOMEN\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-12\"\u003e\u003ca href=\"#cb24-12\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--prioritization_config\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;config/prioritization_profiles.json\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-13\"\u003e\u003ca href=\"#cb24-13\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--prioritizations\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026#39;default\u0026#39;\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-14\"\u003e\u003ca href=\"#cb24-14\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--explode_infos\u003c/span\u003e \u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-15\"\u003e\u003ca href=\"#cb24-15\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e \u003cspan class=\"at\"\u003e--query\u003c/span\u003e\u003cspan class=\"op\"\u003e=\u003c/span\u003e\u003cspan class=\"st\"\u003e\u0026quot;SELECT NOMEN, PZFlag, PZScore \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-16\"\u003e\u003ca href=\"#cb24-16\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e FROM variants \u003c/span\u003e\u003cspan class=\"dt\"\u003e\\\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb24-17\"\u003e\u003ca href=\"#cb24-17\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"st\"\u003e ORDER BY PZScore DESC\u0026quot;\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"sourceCode\" id=\"cb25\"\u003e\u003cpre\nclass=\"sourceCode ts\"\u003e\u003ccode class=\"sourceCode typescript\"\u003e\u003cspan id=\"cb25-1\"\u003e\u003ca href=\"#cb25-1\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e NOMEN PZFlag PZScore\u003c/span\u003e\n\u003cspan id=\"cb25-2\"\u003e\u003ca href=\"#cb25-2\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e0\u003c/span\u003e WASH7P\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_024540\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e50\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e585\u003c/span\u003e\u003cspan class=\"er\"\u003eT\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG PASS \u003cspan class=\"dv\"\u003e15\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb25-3\"\u003e\u003ca href=\"#cb25-3\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e1\u003c/span\u003e OR4F5\u003cspan class=\"op\"\u003e:\u003c/span\u003eNP_001005484\u003cspan class=\"op\"\u003e:\u003c/span\u003eexon3\u003cspan class=\"op\"\u003e:\u003c/span\u003ec\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e74\u003c/span\u003e\u003cspan class=\"er\"\u003eA\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG\u003cspan class=\"op\"\u003e:\u003c/span\u003ep\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"at\"\u003eGlu25Gly\u003c/span\u003e PASS \u003cspan class=\"dv\"\u003e5\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb25-4\"\u003e\u003ca href=\"#cb25-4\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e2\u003c/span\u003e EGFR\u003cspan class=\"op\"\u003e:\u003c/span\u003eNM_001346897\u003cspan class=\"op\"\u003e:\u003c/span\u003eexon19\u003cspan class=\"op\"\u003e:\u003c/span\u003ec\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e2226\u003c/span\u003e\u003cspan class=\"er\"\u003eG\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eA\u003cspan class=\"op\"\u003e:\u003c/span\u003ep\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"at\"\u003eGln742Gln\u003c/span\u003e PASS \u003cspan class=\"dv\"\u003e5\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb25-5\"\u003e\u003ca href=\"#cb25-5\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e3\u003c/span\u003e LINC01128\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_047526\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e287\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e3767\u003c/span\u003e\u003cspan class=\"er\"\u003eA\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG PASS \u003cspan class=\"dv\"\u003e0\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb25-6\"\u003e\u003ca href=\"#cb25-6\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e4\u003c/span\u003e LINC01128\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_047526\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e287\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e3768\u003c/span\u003e\u003cspan class=\"er\"\u003eA\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG PASS \u003cspan class=\"dv\"\u003e0\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb25-7\"\u003e\u003ca href=\"#cb25-7\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e5\u003c/span\u003e LINC01128\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_047526\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e287\u003c/span\u003e\u003cspan class=\"op\"\u003e+\u003c/span\u003e\u003cspan class=\"dv\"\u003e3769\u003c/span\u003e\u003cspan class=\"er\"\u003eA\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG PASS \u003cspan class=\"dv\"\u003e0\u003c/span\u003e\u003c/span\u003e\n\u003cspan id=\"cb25-8\"\u003e\u003ca href=\"#cb25-8\" aria-hidden=\"true\" tabindex=\"-1\"\u003e\u003c/a\u003e\u003cspan class=\"dv\"\u003e6\u003c/span\u003e FAM138A\u003cspan class=\"op\"\u003e:\u003c/span\u003eNR_026818\u003cspan class=\"op\"\u003e:\u003c/span\u003eexon3\u003cspan class=\"op\"\u003e:\u003c/span\u003en\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"dv\"\u003e597\u003c/span\u003e\u003cspan class=\"er\"\u003eT\u003c/span\u003e\u003cspan class=\"op\"\u003e\u0026gt;\u003c/span\u003eG\u003cspan class=\"op\"\u003e:\u003c/span\u003ep\u003cspan class=\"op\"\u003e.\u003c/span\u003e\u003cspan class=\"at\"\u003eTyr199Asp\u003c/span\u003e FILTERED \u003cspan class=\"op\"\u003e-\u003c/span\u003e\u003cspan class=\"dv\"\u003e100\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/blockquote\u003e\n\u003c/details\u003e\n\u003ch1 data-number=\"4\" id=\"documentation\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e4\u003c/span\u003e Documentation\u003c/h1\u003e\n\u003cp\u003e\u003ca href=\"docs/user_guide.html\"\u003eHOWARD User Guide\u003c/a\u003e is available to\nassist users for particular commands, such as software installation,\ndatabases download, annotation command, and so on.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"docs/tips.html\"\u003eHOWARD Tips\u003c/a\u003e proposes some additional\nadvices to handle HOWARD for particular use cases.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"docs/help.html\"\u003eHOWARD Help\u003c/a\u003e describes options of all\nHOWARD tools. All information are also available for each tool using\n\u003ccode\u003e--help\u003c/code\u003e option.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"docs/help.configuration.html\"\u003eHOWARD Configuration JSON\u003c/a\u003e\ndescribes configuration JSON file structure and options.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"docs/help.parameters.html\"\u003eHOWARD Parameters JSON\u003c/a\u003e\ndescribes parameters JSON file structure and options.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"docs/help.parameters.databases.html\"\u003eHOWARD Parameters\nDatabases JSON\u003c/a\u003e describes configuration JSON file for databases\ndownload and convert.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"plugins/README.html\"\u003eHOWARD Plugins\u003c/a\u003e describes how to\ncreate HOWARD plugins.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"docs/pdoc/index.html\"\u003eHOWARD Package\u003c/a\u003e describes HOWARD\nPackage, Classes and Functions.\u003c/p\u003e\n\u003ch1 data-number=\"5\" id=\"contact\"\u003e\u003cspan\nclass=\"header-section-number\"\u003e5\u003c/span\u003e Contact\u003c/h1\u003e\n\u003cp\u003e\u003ca\nhref=\"https://www.chru-strasbourg.fr/service/bioinformatique-medicale-appliquee-au-diagnostic-unite-de/\"\u003eMedical\nBioinformatics applied to Diagnosis Lab\u003c/a\u003e @ Strasbourg Univerty\nHospital\u003c/p\u003e\n\u003cp\u003e\u003ca\nhref=\"bioinfo@chru-strasbourg.fr\"\u003ebioinfo@chru-strasbourg.fr\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"https://github.com/bioinfo-chru-strasbourg\"\u003eGitHub\u003c/a\u003e\u003c/p\u003e\n\u003c/body\u003e\n\u003c/html\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinfo-chru-strasbourg%2Fhoward","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioinfo-chru-strasbourg%2Fhoward","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinfo-chru-strasbourg%2Fhoward/lists"}