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GitHub - Ensembl/ensembl-vep: The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
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0-1.14-.243-1.847-.705-2.319-.477-.488-1.319-.862-2.824-1.025-1.487-.161-2.192.138-2.533.529-.269.307-.437.808-.438 1.578v.021c0 .265.021.562.063.893Zm-1.626 0c.042-.331.063-.628.063-.894v-.02c-.001-.77-.169-1.271-.438-1.578-.341-.391-1.046-.69-2.533-.529-1.505.163-2.347.537-2.824 1.025-.462.472-.705 1.179-.705 2.319 0 1.211.175 1.926.558 2.361.365.414 1.084.751 2.657.751 1.21 0 1.902-.394 2.344-.938.475-.584.742-1.44.878-2.497Z"></path><path d="M14.5 14.25a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Zm-5 0a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Z"></path> </svg> <div> <div class="color-fg-default h4">GitHub Copilot</div> Write better code with AI </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"security","context":"product","tag":"link","label":"security_link_product_navbar"}" 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dir=\"auto\"\u003eensembl-vep\u003c/h1\u003e\u003ca id=\"user-content-ensembl-vep\" class=\"anchor\" aria-label=\"Permalink: ensembl-vep\" href=\"#ensembl-vep\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ca 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100%;\"\u003e\u003c/a\u003e\n\u003ca href=\"https://hub.docker.com/r/ensemblorg/ensembl-vep\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/dd14c574fbc926865da860cee48fda7b3627267fd1efcc465994ab0f43e6d053/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f616374696f6e732f776f726b666c6f772f7374617475732f456e73656d626c2f656e73656d626c2d7665702f646f636b65722e796d6c3f6c6162656c3d646f636b65722532306275696c64\" alt=\"Docker Build Status\" data-canonical-src=\"https://img.shields.io/github/actions/workflow/status/Ensembl/ensembl-vep/docker.yml?label=docker%20build\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003ca href=\"https://hub.docker.com/r/ensemblorg/ensembl-vep\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/db62b54ebb9ccd88116928da475fd7d9108235d00956890598753286310e294c/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f656e73656d626c6f72672f656e73656d626c2d7665702e737667\" alt=\"Docker Hub Pulls\" data-canonical-src=\"https://img.shields.io/docker/pulls/ensemblorg/ensembl-vep.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003cstrong\u003eVEP\u003c/strong\u003e (Variant Effect Predictor) predicts the functional effects of genomic variants.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eHaplosaurus\u003c/strong\u003e uses phased genotype data to predict whole-transcript haplotype sequences.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eVariant Recoder\u003c/strong\u003e translates between different variant encodings.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch5 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eTable of contents\u003c/h5\u003e\u003ca id=\"user-content-table-of-contents\" class=\"anchor\" aria-label=\"Permalink: Table of contents\" href=\"#table-of-contents\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#install\"\u003eInstallation and requirements\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#vep\"\u003eVEP\u003c/a\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#vepusage\"\u003eUsage\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#haplo\"\u003eHaplosaurus\u003c/a\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#haplousage\"\u003eUsage\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#haplooutput\"\u003eOutput\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#haploREST\"\u003eREST\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#haploflags\"\u003eFlags\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#recoder\"\u003eVariant Recoder\u003c/a\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#recoderusage\"\u003eUsage\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#recoderoutput\"\u003eOutput\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003chr\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-install\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstallation and requirements\u003c/h3\u003e\u003ca id=\"user-content-installation-and-requirements\" class=\"anchor\" aria-label=\"Permalink: Installation and requirements\" href=\"#installation-and-requirements\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe VEP package requires:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003cstrong\u003egcc\u003c/strong\u003e, \u003cstrong\u003eg++\u003c/strong\u003e and \u003cstrong\u003emake\u003c/strong\u003e\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ePerl\u003c/strong\u003e (\u0026gt;=5.10 recommended, tested on 5.10, 5.14, 5.18, 5.22, 5.26)\u003c/li\u003e\n\u003cli\u003ePerl libraries \u003ca href=\"https://metacpan.org/pod/Archive::Zip\" rel=\"nofollow\"\u003eArchive::Zip\u003c/a\u003e and \u003ca href=\"https://metacpan.org/pod/DBI\" rel=\"nofollow\"\u003eDBI\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eThe remaining dependencies can be installed using the included \u003ca href=\"http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer\" rel=\"nofollow\"\u003eINSTALL.pl\u003c/a\u003e script. Basic instructions:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"git clone https://github.com/Ensembl/ensembl-vep.git\ncd ensembl-vep\nperl INSTALL.pl\"\u003e\u003cpre\u003egit clone https://github.com/Ensembl/ensembl-vep.git\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e ensembl-vep\nperl INSTALL.pl\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe installer may also be used to check for updates to this and co-dependent packages, simply re-run INSTALL.pl.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eSee \u003ca href=\"http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html\" rel=\"nofollow\"\u003edocumentation\u003c/a\u003e for full installation instructions.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch4 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eAdditional CPAN modules\u003c/h4\u003e\u003ca id=\"user-content-additional-cpan-modules\" class=\"anchor\" aria-label=\"Permalink: Additional CPAN modules\" href=\"#additional-cpan-modules\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe following modules are optional but most users will benefit from installing them. We recommend using \u003ca href=\"http://search.cpan.org/~miyagawa/Menlo-1.9003/script/cpanm-menlo\" rel=\"nofollow\"\u003ecpanminus\u003c/a\u003e to install.\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"http://search.cpan.org/~michielb/DBD-mysql/lib/DBD/mysql.pm\" rel=\"nofollow\"\u003eDBD::mysql\u003c/a\u003e - required for database access (\u003ccode\u003e--database\u003c/code\u003e or \u003ccode\u003e--cache\u003c/code\u003e without \u003ccode\u003e--offline\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://search.cpan.org/~benbooth/Set-IntervalTree/lib/Set/IntervalTree.pm\" rel=\"nofollow\"\u003eSet::IntervalTree\u003c/a\u003e - required for Haplosaurus, also confers speed updates to VEP\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://search.cpan.org/dist/JSON/\" rel=\"nofollow\"\u003eJSON\u003c/a\u003e - required for writing JSON output\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://search.cpan.org/~nwclark/PerlIO-gzip-0.19/gzip.pm\" rel=\"nofollow\"\u003ePerlIO::gzip\u003c/a\u003e - faster compressed file parsing\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://search.cpan.org/~lds/Bio-BigFile-1.07/lib/Bio/DB/BigFile.pm\" rel=\"nofollow\"\u003eBio::DB::BigFile\u003c/a\u003e - required for reading custom annotation data from BigWig files\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch4 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDocker\u003c/h4\u003e\u003ca id=\"user-content-docker\" class=\"anchor\" aria-label=\"Permalink: Docker\" href=\"#docker\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eA docker image for VEP is available from \u003ca href=\"https://hub.docker.com/r/ensemblorg/ensembl-vep\" rel=\"nofollow\"\u003eDockerHub\u003c/a\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eSee \u003ca href=\"http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker\" rel=\"nofollow\"\u003edocumentation\u003c/a\u003e for the Docker installation instructions.\u003c/p\u003e\n\u003chr\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-vep\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eVEP\u003c/h2\u003e\u003ca id=\"user-content-vep\" class=\"anchor\" aria-label=\"Permalink: VEP\" href=\"#vep\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-vepusage\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eUsage\u003c/h3\u003e\u003ca id=\"user-content-usage\" class=\"anchor\" aria-label=\"Permalink: Usage\" href=\"#usage\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"./vep -i input.vcf -o out.txt -offline\"\u003e\u003cpre\u003e./vep -i input.vcf -o out.txt -offline\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eSee \u003ca href=\"http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic\" rel=\"nofollow\"\u003edocumentation\u003c/a\u003e for full command line instructions.\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cp dir=\"auto\"\u003ePlease report any bugs or issues by \u003ca href=\"http://www.ensembl.org/info/about/contact/index.html\" rel=\"nofollow\"\u003econtacting Ensembl\u003c/a\u003e or creating a \u003ca href=\"https://github.com/Ensembl/ensembl-vep/issues\"\u003eGitHub issue\u003c/a\u003e\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003chr\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-haplo\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eHaplosaurus\u003c/h2\u003e\u003ca id=\"user-content-haplosaurus\" class=\"anchor\" aria-label=\"Permalink: Haplosaurus\" href=\"#haplosaurus\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ccode\u003ehaplo\u003c/code\u003e is a local tool implementation of the same functionality that powers the \u003ca href=\"http://www.ensembl.org/Homo_sapiens/Transcript/Haplotypes?t=ENST00000304748\" rel=\"nofollow\"\u003eEnsembl transcript haplotypes view\u003c/a\u003e. It takes phased genotypes from a VCF and constructs a pair of haplotype sequences for each overlapped transcript; these sequences are also translated into predicted protein haplotype sequences. Each variant haplotype sequence is aligned and compared to the reference, and an HGVS-like name is constructed representing its differences to the reference.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThis approach offers an advantage over VEP's analysis, which treats each input variant independently. By considering the combined change contributed by all the variant alleles across a transcript, the compound effects the variants may have are correctly accounted for.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003ccode\u003ehaplo\u003c/code\u003e shares much of the same command line functionality with \u003ccode\u003evep\u003c/code\u003e, and can use VEP caches, Ensembl databases, GFF and GTF files as sources of transcript data; all \u003ccode\u003evep\u003c/code\u003e command line flags relating to this functionality work the same with \u003ccode\u003ehaplo\u003c/code\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-haplousage\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eUsage\u003c/h3\u003e\u003ca id=\"user-content-usage-1\" class=\"anchor\" aria-label=\"Permalink: Usage\" href=\"#usage-1\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eInput data must be a \u003ca href=\"http://samtools.github.io/hts-specs/VCFv4.3.pdf\" rel=\"nofollow\"\u003eVCF\u003c/a\u003e containing phased genotype data for at least one individual and file must be sorted by chromosome and genomic position; no other formats are currently supported.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eWhen using a VEP cache as the source of transcript annotation, the first time you run \u003ccode\u003ehaplo\u003c/code\u003e with a particular cache it will spend some time scanning transcript locations in the cache.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"./haplo -i input.vcf -o out.txt -cache\"\u003e\u003cpre\u003e./haplo -i input.vcf -o out.txt -cache\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-haplooutput\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eOutput\u003c/h3\u003e\u003ca id=\"user-content-output\" class=\"anchor\" aria-label=\"Permalink: Output\" href=\"#output\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe default output format is a simple tab-delimited file reporting all observed non-reference haplotypes. It has the following fields:\u003c/p\u003e\n\u003col dir=\"auto\"\u003e\n\u003cli\u003eTranscript stable ID\u003c/li\u003e\n\u003cli\u003eCDS haplotype name\u003c/li\u003e\n\u003cli\u003eComma-separated list of \u003ca href=\"#haploflags\"\u003eflags\u003c/a\u003e for CDS haplotype\u003c/li\u003e\n\u003cli\u003eProtein haplotype name\u003c/li\u003e\n\u003cli\u003eComma-separated list of \u003ca href=\"#haploflags\"\u003eflags\u003c/a\u003e for protein haplotype\u003c/li\u003e\n\u003cli\u003eComma-separated list of frequency data for protein haplotype\u003c/li\u003e\n\u003cli\u003eComma-separated list of contributing variants\u003c/li\u003e\n\u003cli\u003eComma-separated list of sample:count that exhibit this haplotype\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp dir=\"auto\"\u003eThe altered haplotype sequences can be obtained by switching to JSON output using \u003ccode\u003e--json\u003c/code\u003e which will display them by default.\nEach transcript analysed is summarised as a JSON object written to one line of the output file.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThe \u003ca href=\"#haploREST\"\u003eJSON output\u003c/a\u003e structure matches the format of the \u003ca href=\"https://rest.ensembl.org/documentation/info/transcript_haplotypes_get\" rel=\"nofollow\"\u003etranscript haplotype REST endpoint\u003c/a\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eYou may exclude fields in the JSON from being exported with \u003ccode\u003e--dont_export field1,field2\u003c/code\u003e. This may be used, for example, to exclude the full haplotype sequence and aligned sequences from the output with \u003ccode\u003e--dont_export seq,aligned_sequences\u003c/code\u003e.\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cp dir=\"auto\"\u003eNote JSON output does not currently include side-loaded frequency data.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-haplorest\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eREST service\u003c/h3\u003e\u003ca id=\"user-content-rest-service\" class=\"anchor\" aria-label=\"Permalink: REST service\" href=\"#rest-service\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe \u003ca href=\"https://rest.ensembl.org/documentation/info/transcript_haplotypes_get\" rel=\"nofollow\"\u003etranscript haplotype REST endpoint\u003c/a\u003e.\nreturns arrays of protein_haplotypes and cds_haplotypes for a given transcript. The default haplotype record includes:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003cstrong\u003epopulation_counts\u003c/strong\u003e: the number of times the haplotype is seen in each population\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003epopulation_frequencies\u003c/strong\u003e: the frequency of the haplotype in each population\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003econtributing_variants\u003c/strong\u003e: variants contributing to the haplotype\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ediffs\u003c/strong\u003e: differences between the reference and this haplotype\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ehex\u003c/strong\u003e: the md5 hex of this haplotype sequence\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eother_hexes\u003c/strong\u003e: the md5 hex of other related haplotype sequences (\nCDSHaplotypes that translate to this ProteinHaplotype or\nProteinHaplotype representing the translation of this CDSHaplotype)\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ehas_indel\u003c/strong\u003e: does the haplotype contain insertions or deletions\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003etype\u003c/strong\u003e: the type of haplotype - cds, protein\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ename\u003c/strong\u003e: a human readable name for the haplotype (sequence id + REF or a change description)\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eflags\u003c/strong\u003e: \u003ca href=\"#haploflags\"\u003eflags\u003c/a\u003e for the haplotype\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003efrequency\u003c/strong\u003e: haplotype frequency in full sample set\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ecount\u003c/strong\u003e: haplotype count in full sample set\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eThe REST service does not return raw sequences, sample-haplotype assignments and the aligned sequences used to generate\ndifferences by default.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-haploflags\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eFlags\u003c/h3\u003e\u003ca id=\"user-content-flags\" class=\"anchor\" aria-label=\"Permalink: Flags\" href=\"#flags\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eHaplotypes may be flagged with one or more of the following:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003cstrong\u003eindel\u003c/strong\u003e: haplotype contains an insertion or deletion (indel) relative to the reference.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eframeshift:\u003c/strong\u003e haplotype contains at least one indel that disrupts the reading frame of the transcript.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eresolved_frameshift:\u003c/strong\u003e haplotype contains two or more indels whose combined effect restores the reading frame of the transcript.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003estop_changed:\u003c/strong\u003e indicates either a STOP codon is gained (protein truncating variant, PTV) or the existing reference STOP codon is lost.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003edeleterious_sift_or_polyphen:\u003c/strong\u003e haplotype contains at least one single amino acid substitution event flagged as deleterious (SIFT) or probably damaging (PolyPhen2).\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-bioperl-ext\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003ebioperl-ext\u003c/h3\u003e\u003ca id=\"user-content-bioperl-ext\" class=\"anchor\" aria-label=\"Permalink: bioperl-ext\" href=\"#bioperl-ext\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ccode\u003ehaplo\u003c/code\u003e can make use of a fast compiled alignment algorithm from the \u003ca href=\"https://github.com/bioperl/bioperl-ext\"\u003ebioperl-ext\u003c/a\u003e package; this can speed up analysis, particularly in longer transcripts where insertions and/or deletions are introduced. The bioperl-ext package is no longer maintained and requires some tweaking to install. The following instructions install the package in \u003ccode\u003e$HOME/perl5\u003c/code\u003e; edit \u003ccode\u003ePREFIX=[path]\u003c/code\u003e to change this. You may also need to edit the \u003ccode\u003eexport\u003c/code\u003e command to point to the path created for the architecture on your machine.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"git clone https://github.com/bioperl/bioperl-ext.git\ncd bioperl-ext/Bio/Ext/Align/\nperl -pi -e\u0026quot;s|(cd libs.+)CFLAGS=\\\\\\'|\\$1CFLAGS=\\\\\\'-fPIC |\u0026quot; Makefile.PL\nperl Makefile.PL PREFIX=~/perl5\nmake\nmake install\ncd -\nexport PERL5LIB=${PERL5LIB}:${HOME}/perl5/lib/x86_64-linux-gnu/perl/5.22.1/\"\u003e\u003cpre\u003egit clone https://github.com/bioperl/bioperl-ext.git\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e bioperl-ext/Bio/Ext/Align/\nperl -pi -e\u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003es|(cd libs.+)CFLAGS=\u003cspan class=\"pl-cce\"\u003e\\\\\u003c/span\u003e\\'|\u003cspan class=\"pl-cce\"\u003e\\$\u003c/span\u003e1CFLAGS=\u003cspan class=\"pl-cce\"\u003e\\\\\u003c/span\u003e\\'-fPIC |\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e Makefile.PL\nperl Makefile.PL PREFIX=\u003cspan class=\"pl-k\"\u003e~\u003c/span\u003e/perl5\nmake\nmake install\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e -\n\u003cspan class=\"pl-k\"\u003eexport\u003c/span\u003e PERL5LIB=\u003cspan class=\"pl-smi\"\u003e${PERL5LIB}\u003c/span\u003e:\u003cspan class=\"pl-smi\"\u003e${HOME}\u003c/span\u003e/perl5/lib/x86_64-linux-gnu/perl/5.22.1/\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf successful the following should print \u003ccode\u003eOK\u003c/code\u003e:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"perl -MBio::Tools::dpAlign -e\u0026quot;print qq{OK\\n}\u0026quot;\"\u003e\u003cpre\u003eperl -MBio::Tools::dpAlign -e\u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eprint qq{OK\\n}\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003chr\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-recoder\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eVariant Recoder\u003c/h2\u003e\u003ca id=\"user-content-variant-recoder\" class=\"anchor\" aria-label=\"Permalink: Variant Recoder\" href=\"#variant-recoder\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ccode\u003evariant_recoder\u003c/code\u003e is a tool for translating between different variant encodings. It accepts as input any format supported by VEP (VCF, variant ID, HGVS), with extensions to allow for parsing of potentially ambiguous HGVS notations. For each input variant, \u003ccode\u003evariant_recoder\u003c/code\u003e reports all possible encodings including variant IDs from \u003ca href=\"http://www.ensembl.org/info/genome/variation/species/sources_documentation.html\" rel=\"nofollow\"\u003eall sources imported into the Ensembl database\u003c/a\u003e and HGVS (genomic, transcript and protein), reported on Ensembl, RefSeq and LRG sequences.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-recoderusage\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eUsage\u003c/h3\u003e\u003ca id=\"user-content-usage-2\" class=\"anchor\" aria-label=\"Permalink: Usage\" href=\"#usage-2\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ccode\u003evariant_recoder\u003c/code\u003e depends on database access for identifier lookup, and cannot be used in offline mode as per VEP. The output format is JSON and the \u003ca href=\"http://search.cpan.org/dist/JSON/\" rel=\"nofollow\"\u003eJSON perl module\u003c/a\u003e is required.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"./variant_recoder --id [input_data_string]\n./variant_recoder -i [input_file] --species [species]\"\u003e\u003cpre\u003e./variant_recoder --id [input_data_string]\n./variant_recoder -i [input_file] --species [species]\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-recoderoutput\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eOutput\u003c/h3\u003e\u003ca id=\"user-content-output-1\" class=\"anchor\" aria-label=\"Permalink: Output\" href=\"#output-1\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eOutput is a JSON array of objects, one per input variant, with the following keys:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003cstrong\u003einput\u003c/strong\u003e: input string\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eid\u003c/strong\u003e: variant identifiers\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ehgvsg\u003c/strong\u003e: HGVS genomic nomenclature\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ehgvsc\u003c/strong\u003e: HGVS transcript nomenclature\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ehgvsp\u003c/strong\u003e: HGVS protein nomenclature\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003espdi\u003c/strong\u003e: Genomic SPDI notation\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003evcf_string\u003c/strong\u003e: VCF format (optional)\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003evar_synonyms\u003c/strong\u003e: Variation synonyms (optional)\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003emane_select\u003c/strong\u003e: MANE Select transcripts (optional)\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ewarnings\u003c/strong\u003e: Warnings generated e.g. for invalid HGVS\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eUse \u003ccode\u003e--pretty\u003c/code\u003e to pre-format and indent JSON output.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eExample output:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"./variant_recoder --id \u0026quot;AGT:p.Met259Thr\u0026quot; --pretty\n[\n {\n \u0026quot;warnings\u0026quot; : [\n \u0026quot;Possible invalid use of gene or protein identifier 'AGT' as HGVS reference; AGT:p.Met259Thr may resolve to multiple genomic locations\u0026quot;\n ],\n \u0026quot;C\u0026quot; : {\n \u0026quot;input\u0026quot; : \u0026quot;AGT:p.Met259Thr\u0026quot;,\n \u0026quot;id\u0026quot; : [\n \u0026quot;rs699\u0026quot;,\n \u0026quot;CM920010\u0026quot;,\n \u0026quot;COSV64184214\u0026quot;\n ],\n \u0026quot;hgvsg\u0026quot; : [\n \u0026quot;NC_000001.11:g.230710048A\u0026gt;G\u0026quot;\n ],\n \u0026quot;hgvsc\u0026quot; : [\n \u0026quot;ENST00000366667.6:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000679684.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000679738.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000679802.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000679854.1:n.1287T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000679957.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000680041.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000680783.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000681269.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000681347.1:n.1287T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000681514.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;ENST00000681772.1:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;NM_001382817.3:c.776T\u0026gt;C\u0026quot;,\n \u0026quot;NM_001384479.1:c.776T\u0026gt;C\u0026quot;\n ],\n \u0026quot;hgvsp\u0026quot; : [\n \u0026quot;ENSP00000355627.5:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000505981.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000505063.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000505184.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000506646.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000504866.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000506329.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000505985.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000505963.1:p.Met259Thr\u0026quot;,\n \u0026quot;ENSP00000505829.1:p.Met259Thr\u0026quot;,\n \u0026quot;NP_001369746.2:p.Met259Thr\u0026quot;,\n \u0026quot;NP_001371408.1:p.Met259Thr\u0026quot;\n ],\n \u0026quot;spdi\u0026quot; : [\n \u0026quot;NC_000001.11:230710047:A:G\u0026quot;\n ]\n }\n }\n]\"\u003e\u003cpre\u003e./variant_recoder --id \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eAGT:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e --pretty\n[\n {\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003ewarnings\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e [\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003ePossible invalid use of gene or protein identifier 'AGT' as HGVS reference; AGT:p.Met259Thr may resolve to multiple genomic locations\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n ],\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eC\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e {\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003einput\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eAGT:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eid\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e [\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003ers699\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eCM920010\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eCOSV64184214\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n ],\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003ehgvsg\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e [\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eNC_000001.11:g.230710048A\u0026gt;G\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n ],\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003ehgvsc\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e [\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000366667.6:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000679684.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000679738.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000679802.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000679854.1:n.1287T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000679957.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000680041.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000680783.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000681269.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000681347.1:n.1287T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000681514.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENST00000681772.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eNM_001382817.3:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eNM_001384479.1:c.776T\u0026gt;C\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n ],\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003ehgvsp\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e [\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000355627.5:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000505981.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000505063.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000505184.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000506646.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000504866.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000506329.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000505985.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000505963.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eENSP00000505829.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eNP_001369746.2:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e,\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eNP_001371408.1:p.Met259Thr\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n ],\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003espdi\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c1\"\u003e:\u003c/span\u003e [\n \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eNC_000001.11:230710047:A:G\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n ]\n }\n }\n]\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ca name=\"user-content-recoderopts\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eOptions\u003c/h3\u003e\u003ca id=\"user-content-options\" class=\"anchor\" aria-label=\"Permalink: Options\" href=\"#options\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ccode\u003evariant_recoder\u003c/code\u003e shares many of the same command line flags as VEP. Others are unique to \u003ccode\u003evariant_recoder\u003c/code\u003e.\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ccode\u003e-id|--input_data [input_string]\u003c/code\u003e: a single variant as a string.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e-i|--input_file [input_file]\u003c/code\u003e: input file containing one or more variants, one per line. Mixed formats disallowed.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--species\u003c/code\u003e: species to use (default: homo_sapiens).\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--grch37\u003c/code\u003e: use GRCh37 assembly instead of GRCh38.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--genomes\u003c/code\u003e: set database parameters for \u003ca href=\"http://ensemblgenomes.org/\" rel=\"nofollow\"\u003eEnsembl Genomes\u003c/a\u003e species.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--pretty\u003c/code\u003e: write pre-formatted indented JSON.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--fields [field1,field2]\u003c/code\u003e: limit output fields. Comma-separated list, one or more of: \u003ccode\u003eid\u003c/code\u003e, \u003ccode\u003ehgvsg\u003c/code\u003e, \u003ccode\u003ehgvsc\u003c/code\u003e, \u003ccode\u003ehgvsp\u003c/code\u003e, \u003ccode\u003espdi\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--vcf_string\u003c/code\u003e : report VCF\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--var_synonyms\u003c/code\u003e : report variation synonyms\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--mane_select\u003c/code\u003e : report MANE Select transcripts in HGVS format\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--host [db_host]\u003c/code\u003e: change database host from default \u003ccode\u003eensembldb.ensembl.org\u003c/code\u003e (UK); geographic mirrors are \u003ccode\u003euseastdb.ensembl.org\u003c/code\u003e (US East Coast) and \u003ccode\u003easiadb.ensembl.org\u003c/code\u003e (Asia). \u003ccode\u003e--user\u003c/code\u003e, \u003ccode\u003e--port\u003c/code\u003e and \u003ccode\u003e--pass\u003c/code\u003e may also be set.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--pick\u003c/code\u003e, \u003ccode\u003e--per_gene\u003c/code\u003e, \u003ccode\u003e--pick_allele\u003c/code\u003e, \u003ccode\u003e--pick_allele_gene\u003c/code\u003e, \u003ccode\u003e--pick_order\u003c/code\u003e: set and customise transcript selection process, see \u003ca href=\"http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick\" rel=\"nofollow\"\u003eVEP documentation\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/article\u003e","loaded":true,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":[{"level":1,"text":"ensembl-vep","anchor":"ensembl-vep","htmlText":"ensembl-vep"},{"level":5,"text":"Table of contents","anchor":"table-of-contents","htmlText":"Table of contents"},{"level":3,"text":"Installation and requirements","anchor":"installation-and-requirements","htmlText":"Installation and requirements"},{"level":4,"text":"Additional CPAN modules","anchor":"additional-cpan-modules","htmlText":"Additional CPAN modules"},{"level":4,"text":"Docker","anchor":"docker","htmlText":"Docker"},{"level":2,"text":"VEP","anchor":"vep","htmlText":"VEP"},{"level":3,"text":"Usage","anchor":"usage","htmlText":"Usage"},{"level":2,"text":"Haplosaurus","anchor":"haplosaurus","htmlText":"Haplosaurus"},{"level":3,"text":"Usage","anchor":"usage-1","htmlText":"Usage"},{"level":3,"text":"Output","anchor":"output","htmlText":"Output"},{"level":3,"text":"REST service","anchor":"rest-service","htmlText":"REST service"},{"level":3,"text":"Flags","anchor":"flags","htmlText":"Flags"},{"level":3,"text":"bioperl-ext","anchor":"bioperl-ext","htmlText":"bioperl-ext"},{"level":2,"text":"Variant Recoder","anchor":"variant-recoder","htmlText":"Variant 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0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><a href="https://github.com/Ensembl/ensembl-vep/blob/release/113/LICENSE"><img src="https://camo.githubusercontent.com/eae3f779e46b3425baf0f872451678e2d35f482961b11e064b64ab95655dfabe/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f6c6963656e73652f456e73656d626c2f656e73656d626c2d7665702e737667" alt="GitHub" data-canonical-src="https://img.shields.io/github/license/Ensembl/ensembl-vep.svg" style="max-width: 100%;"></a> <a href="https://coveralls.io/github/Ensembl/ensembl-vep?branch=release/113" rel="nofollow"><img src="https://camo.githubusercontent.com/bad7b0e5aabb10707eca882c27673f954e728a18950a5a4b17e08cc9a76c6773/68747470733a2f2f636f766572616c6c732e696f2f7265706f732f6769746875622f456e73656d626c2f656e73656d626c2d7665702f62616467652e7376673f6272616e63683d6d61696e" alt="Coverage Status" data-canonical-src="https://coveralls.io/repos/github/Ensembl/ensembl-vep/badge.svg?branch=main" style="max-width: 100%;"></a> <a href="https://hub.docker.com/r/ensemblorg/ensembl-vep" rel="nofollow"><img src="https://camo.githubusercontent.com/dd14c574fbc926865da860cee48fda7b3627267fd1efcc465994ab0f43e6d053/68747470733a2f2f696d672e736869656c64732e696f2f6769746875622f616374696f6e732f776f726b666c6f772f7374617475732f456e73656d626c2f656e73656d626c2d7665702f646f636b65722e796d6c3f6c6162656c3d646f636b65722532306275696c64" alt="Docker Build Status" data-canonical-src="https://img.shields.io/github/actions/workflow/status/Ensembl/ensembl-vep/docker.yml?label=docker%20build" style="max-width: 100%;"></a> <a href="https://hub.docker.com/r/ensemblorg/ensembl-vep" rel="nofollow"><img src="https://camo.githubusercontent.com/db62b54ebb9ccd88116928da475fd7d9108235d00956890598753286310e294c/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f656e73656d626c6f72672f656e73656d626c2d7665702e737667" alt="Docker Hub Pulls" data-canonical-src="https://img.shields.io/docker/pulls/ensemblorg/ensembl-vep.svg" style="max-width: 100%;"></a></p> <ul dir="auto"> <li><strong>VEP</strong> (Variant Effect Predictor) predicts the functional effects of genomic variants.</li> <li><strong>Haplosaurus</strong> uses phased genotype data to predict whole-transcript haplotype sequences.</li> <li><strong>Variant Recoder</strong> translates between different variant encodings.</li> </ul> <div class="markdown-heading" dir="auto"><h5 tabindex="-1" class="heading-element" dir="auto">Table of contents</h5><a id="user-content-table-of-contents" class="anchor" aria-label="Permalink: Table of contents" href="#table-of-contents"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li><a href="#install">Installation and requirements</a></li> <li><a href="#vep">VEP</a> <ul dir="auto"> <li><a href="#vepusage">Usage</a></li> </ul> </li> <li><a href="#haplo">Haplosaurus</a> <ul dir="auto"> <li><a href="#haplousage">Usage</a></li> <li><a href="#haplooutput">Output</a></li> <li><a href="#haploREST">REST</a></li> <li><a href="#haploflags">Flags</a></li> </ul> </li> <li><a href="#recoder">Variant Recoder</a> <ul dir="auto"> <li><a href="#recoderusage">Usage</a></li> <li><a href="#recoderoutput">Output</a></li> </ul> </li> </ul> <hr> <p dir="auto"><a name="user-content-install"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Installation and requirements</h3><a id="user-content-installation-and-requirements" class="anchor" aria-label="Permalink: Installation and requirements" href="#installation-and-requirements"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The VEP package requires:</p> <ul dir="auto"> <li><strong>gcc</strong>, <strong>g++</strong> and <strong>make</strong></li> <li><strong>Perl</strong> (>=5.10 recommended, tested on 5.10, 5.14, 5.18, 5.22, 5.26)</li> <li>Perl libraries <a href="https://metacpan.org/pod/Archive::Zip" rel="nofollow">Archive::Zip</a> and <a href="https://metacpan.org/pod/DBI" rel="nofollow">DBI</a></li> </ul> <p dir="auto">The remaining dependencies can be installed using the included <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer" rel="nofollow">INSTALL.pl</a> script. Basic instructions:</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="git clone https://github.com/Ensembl/ensembl-vep.git cd ensembl-vep perl INSTALL.pl"><pre>git clone https://github.com/Ensembl/ensembl-vep.git <span class="pl-c1">cd</span> ensembl-vep perl INSTALL.pl</pre></div> <p dir="auto">The installer may also be used to check for updates to this and co-dependent packages, simply re-run INSTALL.pl.</p> <p dir="auto">See <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html" rel="nofollow">documentation</a> for full installation instructions.</p> <div class="markdown-heading" dir="auto"><h4 tabindex="-1" class="heading-element" dir="auto">Additional CPAN modules</h4><a id="user-content-additional-cpan-modules" class="anchor" aria-label="Permalink: Additional CPAN modules" href="#additional-cpan-modules"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The following modules are optional but most users will benefit from installing them. We recommend using <a href="http://search.cpan.org/~miyagawa/Menlo-1.9003/script/cpanm-menlo" rel="nofollow">cpanminus</a> to install.</p> <ul dir="auto"> <li><a href="http://search.cpan.org/~michielb/DBD-mysql/lib/DBD/mysql.pm" rel="nofollow">DBD::mysql</a> - required for database access (<code>--database</code> or <code>--cache</code> without <code>--offline</code>)</li> <li><a href="http://search.cpan.org/~benbooth/Set-IntervalTree/lib/Set/IntervalTree.pm" rel="nofollow">Set::IntervalTree</a> - required for Haplosaurus, also confers speed updates to VEP</li> <li><a href="http://search.cpan.org/dist/JSON/" rel="nofollow">JSON</a> - required for writing JSON output</li> <li><a href="http://search.cpan.org/~nwclark/PerlIO-gzip-0.19/gzip.pm" rel="nofollow">PerlIO::gzip</a> - faster compressed file parsing</li> <li><a href="http://search.cpan.org/~lds/Bio-BigFile-1.07/lib/Bio/DB/BigFile.pm" rel="nofollow">Bio::DB::BigFile</a> - required for reading custom annotation data from BigWig files</li> </ul> <div class="markdown-heading" dir="auto"><h4 tabindex="-1" class="heading-element" dir="auto">Docker</h4><a id="user-content-docker" class="anchor" aria-label="Permalink: Docker" href="#docker"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">A docker image for VEP is available from <a href="https://hub.docker.com/r/ensemblorg/ensembl-vep" rel="nofollow">DockerHub</a>.</p> <p dir="auto">See <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker" rel="nofollow">documentation</a> for the Docker installation instructions.</p> <hr> <p dir="auto"><a name="user-content-vep"></a></p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">VEP</h2><a id="user-content-vep" class="anchor" aria-label="Permalink: VEP" href="#vep"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><a name="user-content-vepusage"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Usage</h3><a id="user-content-usage" class="anchor" aria-label="Permalink: Usage" href="#usage"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="./vep -i input.vcf -o out.txt -offline"><pre>./vep -i input.vcf -o out.txt -offline</pre></div> <p dir="auto">See <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic" rel="nofollow">documentation</a> for full command line instructions.</p> <blockquote> <p dir="auto">Please report any bugs or issues by <a href="http://www.ensembl.org/info/about/contact/index.html" rel="nofollow">contacting Ensembl</a> or creating a <a href="https://github.com/Ensembl/ensembl-vep/issues">GitHub issue</a></p> </blockquote> <hr> <p dir="auto"><a name="user-content-haplo"></a></p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Haplosaurus</h2><a id="user-content-haplosaurus" class="anchor" aria-label="Permalink: Haplosaurus" href="#haplosaurus"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><code>haplo</code> is a local tool implementation of the same functionality that powers the <a href="http://www.ensembl.org/Homo_sapiens/Transcript/Haplotypes?t=ENST00000304748" rel="nofollow">Ensembl transcript haplotypes view</a>. It takes phased genotypes from a VCF and constructs a pair of haplotype sequences for each overlapped transcript; these sequences are also translated into predicted protein haplotype sequences. Each variant haplotype sequence is aligned and compared to the reference, and an HGVS-like name is constructed representing its differences to the reference.</p> <p dir="auto">This approach offers an advantage over VEP's analysis, which treats each input variant independently. By considering the combined change contributed by all the variant alleles across a transcript, the compound effects the variants may have are correctly accounted for.</p> <p dir="auto"><code>haplo</code> shares much of the same command line functionality with <code>vep</code>, and can use VEP caches, Ensembl databases, GFF and GTF files as sources of transcript data; all <code>vep</code> command line flags relating to this functionality work the same with <code>haplo</code>.</p> <p dir="auto"><a name="user-content-haplousage"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Usage</h3><a id="user-content-usage-1" class="anchor" aria-label="Permalink: Usage" href="#usage-1"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Input data must be a <a href="http://samtools.github.io/hts-specs/VCFv4.3.pdf" rel="nofollow">VCF</a> containing phased genotype data for at least one individual and file must be sorted by chromosome and genomic position; no other formats are currently supported.</p> <p dir="auto">When using a VEP cache as the source of transcript annotation, the first time you run <code>haplo</code> with a particular cache it will spend some time scanning transcript locations in the cache.</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="./haplo -i input.vcf -o out.txt -cache"><pre>./haplo -i input.vcf -o out.txt -cache</pre></div> <p dir="auto"><a name="user-content-haplooutput"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Output</h3><a id="user-content-output" class="anchor" aria-label="Permalink: Output" href="#output"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The default output format is a simple tab-delimited file reporting all observed non-reference haplotypes. It has the following fields:</p> <ol dir="auto"> <li>Transcript stable ID</li> <li>CDS haplotype name</li> <li>Comma-separated list of <a href="#haploflags">flags</a> for CDS haplotype</li> <li>Protein haplotype name</li> <li>Comma-separated list of <a href="#haploflags">flags</a> for protein haplotype</li> <li>Comma-separated list of frequency data for protein haplotype</li> <li>Comma-separated list of contributing variants</li> <li>Comma-separated list of sample:count that exhibit this haplotype</li> </ol> <p dir="auto">The altered haplotype sequences can be obtained by switching to JSON output using <code>--json</code> which will display them by default. Each transcript analysed is summarised as a JSON object written to one line of the output file.</p> <p dir="auto">The <a href="#haploREST">JSON output</a> structure matches the format of the <a href="https://rest.ensembl.org/documentation/info/transcript_haplotypes_get" rel="nofollow">transcript haplotype REST endpoint</a>.</p> <p dir="auto">You may exclude fields in the JSON from being exported with <code>--dont_export field1,field2</code>. This may be used, for example, to exclude the full haplotype sequence and aligned sequences from the output with <code>--dont_export seq,aligned_sequences</code>.</p> <blockquote> <p dir="auto">Note JSON output does not currently include side-loaded frequency data.</p> </blockquote> <p dir="auto"><a name="user-content-haplorest"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">REST service</h3><a id="user-content-rest-service" class="anchor" aria-label="Permalink: REST service" href="#rest-service"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The <a href="https://rest.ensembl.org/documentation/info/transcript_haplotypes_get" rel="nofollow">transcript haplotype REST endpoint</a>. returns arrays of protein_haplotypes and cds_haplotypes for a given transcript. The default haplotype record includes:</p> <ul dir="auto"> <li><strong>population_counts</strong>: the number of times the haplotype is seen in each population</li> <li><strong>population_frequencies</strong>: the frequency of the haplotype in each population</li> <li><strong>contributing_variants</strong>: variants contributing to the haplotype</li> <li><strong>diffs</strong>: differences between the reference and this haplotype</li> <li><strong>hex</strong>: the md5 hex of this haplotype sequence</li> <li><strong>other_hexes</strong>: the md5 hex of other related haplotype sequences ( CDSHaplotypes that translate to this ProteinHaplotype or ProteinHaplotype representing the translation of this CDSHaplotype)</li> <li><strong>has_indel</strong>: does the haplotype contain insertions or deletions</li> <li><strong>type</strong>: the type of haplotype - cds, protein</li> <li><strong>name</strong>: a human readable name for the haplotype (sequence id + REF or a change description)</li> <li><strong>flags</strong>: <a href="#haploflags">flags</a> for the haplotype</li> <li><strong>frequency</strong>: haplotype frequency in full sample set</li> <li><strong>count</strong>: haplotype count in full sample set</li> </ul> <p dir="auto">The REST service does not return raw sequences, sample-haplotype assignments and the aligned sequences used to generate differences by default.</p> <p dir="auto"><a name="user-content-haploflags"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Flags</h3><a id="user-content-flags" class="anchor" aria-label="Permalink: Flags" href="#flags"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Haplotypes may be flagged with one or more of the following:</p> <ul dir="auto"> <li><strong>indel</strong>: haplotype contains an insertion or deletion (indel) relative to the reference.</li> <li><strong>frameshift:</strong> haplotype contains at least one indel that disrupts the reading frame of the transcript.</li> <li><strong>resolved_frameshift:</strong> haplotype contains two or more indels whose combined effect restores the reading frame of the transcript.</li> <li><strong>stop_changed:</strong> indicates either a STOP codon is gained (protein truncating variant, PTV) or the existing reference STOP codon is lost.</li> <li><strong>deleterious_sift_or_polyphen:</strong> haplotype contains at least one single amino acid substitution event flagged as deleterious (SIFT) or probably damaging (PolyPhen2).</li> </ul> <p dir="auto"><a name="user-content-bioperl-ext"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">bioperl-ext</h3><a id="user-content-bioperl-ext" class="anchor" aria-label="Permalink: bioperl-ext" href="#bioperl-ext"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><code>haplo</code> can make use of a fast compiled alignment algorithm from the <a href="https://github.com/bioperl/bioperl-ext">bioperl-ext</a> package; this can speed up analysis, particularly in longer transcripts where insertions and/or deletions are introduced. The bioperl-ext package is no longer maintained and requires some tweaking to install. The following instructions install the package in <code>$HOME/perl5</code>; edit <code>PREFIX=[path]</code> to change this. You may also need to edit the <code>export</code> command to point to the path created for the architecture on your machine.</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="git clone https://github.com/bioperl/bioperl-ext.git cd bioperl-ext/Bio/Ext/Align/ perl -pi -e"s|(cd libs.+)CFLAGS=\\\'|\$1CFLAGS=\\\'-fPIC |" Makefile.PL perl Makefile.PL PREFIX=~/perl5 make make install cd - export PERL5LIB=${PERL5LIB}:${HOME}/perl5/lib/x86_64-linux-gnu/perl/5.22.1/"><pre>git clone https://github.com/bioperl/bioperl-ext.git <span class="pl-c1">cd</span> bioperl-ext/Bio/Ext/Align/ perl -pi -e<span class="pl-s"><span class="pl-pds">"</span>s|(cd libs.+)CFLAGS=<span class="pl-cce">\\</span>\'|<span class="pl-cce">\$</span>1CFLAGS=<span class="pl-cce">\\</span>\'-fPIC |<span class="pl-pds">"</span></span> Makefile.PL perl Makefile.PL PREFIX=<span class="pl-k">~</span>/perl5 make make install <span class="pl-c1">cd</span> - <span class="pl-k">export</span> PERL5LIB=<span class="pl-smi">${PERL5LIB}</span>:<span class="pl-smi">${HOME}</span>/perl5/lib/x86_64-linux-gnu/perl/5.22.1/</pre></div> <p dir="auto">If successful the following should print <code>OK</code>:</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="perl -MBio::Tools::dpAlign -e"print qq{OK\n}""><pre>perl -MBio::Tools::dpAlign -e<span class="pl-s"><span class="pl-pds">"</span>print qq{OK\n}<span class="pl-pds">"</span></span></pre></div> <hr> <p dir="auto"><a name="user-content-recoder"></a></p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Variant Recoder</h2><a id="user-content-variant-recoder" class="anchor" aria-label="Permalink: Variant Recoder" href="#variant-recoder"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><code>variant_recoder</code> is a tool for translating between different variant encodings. It accepts as input any format supported by VEP (VCF, variant ID, HGVS), with extensions to allow for parsing of potentially ambiguous HGVS notations. For each input variant, <code>variant_recoder</code> reports all possible encodings including variant IDs from <a href="http://www.ensembl.org/info/genome/variation/species/sources_documentation.html" rel="nofollow">all sources imported into the Ensembl database</a> and HGVS (genomic, transcript and protein), reported on Ensembl, RefSeq and LRG sequences.</p> <p dir="auto"><a name="user-content-recoderusage"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Usage</h3><a id="user-content-usage-2" class="anchor" aria-label="Permalink: Usage" href="#usage-2"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><code>variant_recoder</code> depends on database access for identifier lookup, and cannot be used in offline mode as per VEP. The output format is JSON and the <a href="http://search.cpan.org/dist/JSON/" rel="nofollow">JSON perl module</a> is required.</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="./variant_recoder --id [input_data_string] ./variant_recoder -i [input_file] --species [species]"><pre>./variant_recoder --id [input_data_string] ./variant_recoder -i [input_file] --species [species]</pre></div> <p dir="auto"><a name="user-content-recoderoutput"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Output</h3><a id="user-content-output-1" class="anchor" aria-label="Permalink: Output" href="#output-1"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Output is a JSON array of objects, one per input variant, with the following keys:</p> <ul dir="auto"> <li><strong>input</strong>: input string</li> <li><strong>id</strong>: variant identifiers</li> <li><strong>hgvsg</strong>: HGVS genomic nomenclature</li> <li><strong>hgvsc</strong>: HGVS transcript nomenclature</li> <li><strong>hgvsp</strong>: HGVS protein nomenclature</li> <li><strong>spdi</strong>: Genomic SPDI notation</li> <li><strong>vcf_string</strong>: VCF format (optional)</li> <li><strong>var_synonyms</strong>: Variation synonyms (optional)</li> <li><strong>mane_select</strong>: MANE Select transcripts (optional)</li> <li><strong>warnings</strong>: Warnings generated e.g. for invalid HGVS</li> </ul> <p dir="auto">Use <code>--pretty</code> to pre-format and indent JSON output.</p> <p dir="auto">Example output:</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="./variant_recoder --id "AGT:p.Met259Thr" --pretty [ { "warnings" : [ "Possible invalid use of gene or protein identifier 'AGT' as HGVS reference; AGT:p.Met259Thr may resolve to multiple genomic locations" ], "C" : { "input" : "AGT:p.Met259Thr", "id" : [ "rs699", "CM920010", "COSV64184214" ], "hgvsg" : [ "NC_000001.11:g.230710048A>G" ], "hgvsc" : [ "ENST00000366667.6:c.776T>C", "ENST00000679684.1:c.776T>C", "ENST00000679738.1:c.776T>C", "ENST00000679802.1:c.776T>C", "ENST00000679854.1:n.1287T>C", "ENST00000679957.1:c.776T>C", "ENST00000680041.1:c.776T>C", "ENST00000680783.1:c.776T>C", "ENST00000681269.1:c.776T>C", "ENST00000681347.1:n.1287T>C", "ENST00000681514.1:c.776T>C", "ENST00000681772.1:c.776T>C", "NM_001382817.3:c.776T>C", "NM_001384479.1:c.776T>C" ], "hgvsp" : [ "ENSP00000355627.5:p.Met259Thr", "ENSP00000505981.1:p.Met259Thr", "ENSP00000505063.1:p.Met259Thr", "ENSP00000505184.1:p.Met259Thr", "ENSP00000506646.1:p.Met259Thr", "ENSP00000504866.1:p.Met259Thr", "ENSP00000506329.1:p.Met259Thr", "ENSP00000505985.1:p.Met259Thr", "ENSP00000505963.1:p.Met259Thr", "ENSP00000505829.1:p.Met259Thr", "NP_001369746.2:p.Met259Thr", "NP_001371408.1:p.Met259Thr" ], "spdi" : [ "NC_000001.11:230710047:A:G" ] } } ]"><pre>./variant_recoder --id <span class="pl-s"><span class="pl-pds">"</span>AGT:p.Met259Thr<span class="pl-pds">"</span></span> --pretty [ { <span class="pl-s"><span class="pl-pds">"</span>warnings<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> [ <span class="pl-s"><span class="pl-pds">"</span>Possible invalid use of gene or protein identifier 'AGT' as HGVS reference; AGT:p.Met259Thr may resolve to multiple genomic locations<span class="pl-pds">"</span></span> ], <span class="pl-s"><span class="pl-pds">"</span>C<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> { <span class="pl-s"><span class="pl-pds">"</span>input<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> <span class="pl-s"><span class="pl-pds">"</span>AGT:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>id<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> [ <span class="pl-s"><span class="pl-pds">"</span>rs699<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>CM920010<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>COSV64184214<span class="pl-pds">"</span></span> ], <span class="pl-s"><span class="pl-pds">"</span>hgvsg<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> [ <span class="pl-s"><span class="pl-pds">"</span>NC_000001.11:g.230710048A>G<span class="pl-pds">"</span></span> ], <span class="pl-s"><span class="pl-pds">"</span>hgvsc<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> [ <span class="pl-s"><span class="pl-pds">"</span>ENST00000366667.6:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000679684.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000679738.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000679802.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000679854.1:n.1287T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000679957.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000680041.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000680783.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000681269.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000681347.1:n.1287T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000681514.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENST00000681772.1:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>NM_001382817.3:c.776T>C<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>NM_001384479.1:c.776T>C<span class="pl-pds">"</span></span> ], <span class="pl-s"><span class="pl-pds">"</span>hgvsp<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> [ <span class="pl-s"><span class="pl-pds">"</span>ENSP00000355627.5:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000505981.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000505063.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000505184.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000506646.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000504866.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000506329.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000505985.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000505963.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>ENSP00000505829.1:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>NP_001369746.2:p.Met259Thr<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>NP_001371408.1:p.Met259Thr<span class="pl-pds">"</span></span> ], <span class="pl-s"><span class="pl-pds">"</span>spdi<span class="pl-pds">"</span></span> <span class="pl-c1">:</span> [ <span class="pl-s"><span class="pl-pds">"</span>NC_000001.11:230710047:A:G<span class="pl-pds">"</span></span> ] } } ]</pre></div> <p dir="auto"><a name="user-content-recoderopts"></a></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Options</h3><a id="user-content-options" class="anchor" aria-label="Permalink: Options" href="#options"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><code>variant_recoder</code> shares many of the same command line flags as VEP. Others are unique to <code>variant_recoder</code>.</p> <ul dir="auto"> <li><code>-id|--input_data [input_string]</code>: a single variant as a string.</li> <li><code>-i|--input_file [input_file]</code>: input file containing one or more variants, one per line. Mixed formats disallowed.</li> <li><code>--species</code>: species to use (default: homo_sapiens).</li> <li><code>--grch37</code>: use GRCh37 assembly instead of GRCh38.</li> <li><code>--genomes</code>: set database parameters for <a href="http://ensemblgenomes.org/" rel="nofollow">Ensembl Genomes</a> species.</li> <li><code>--pretty</code>: write pre-formatted indented JSON.</li> <li><code>--fields [field1,field2]</code>: limit output fields. Comma-separated list, one or more of: <code>id</code>, <code>hgvsg</code>, <code>hgvsc</code>, <code>hgvsp</code>, <code>spdi</code>.</li> <li><code>--vcf_string</code> : report VCF</li> <li><code>--var_synonyms</code> : report variation synonyms</li> <li><code>--mane_select</code> : report MANE Select transcripts in HGVS format</li> <li><code>--host [db_host]</code>: change database host from default <code>ensembldb.ensembl.org</code> (UK); geographic mirrors are <code>useastdb.ensembl.org</code> (US East Coast) and <code>asiadb.ensembl.org</code> (Asia). <code>--user</code>, <code>--port</code> and <code>--pass</code> may also be set.</li> <li><code>--pick</code>, <code>--per_gene</code>, <code>--pick_allele</code>, <code>--pick_allele_gene</code>, <code>--pick_order</code>: set and customise transcript selection process, see <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick" rel="nofollow">VEP documentation</a></li> </ul> </article></div></div></div></div></div> <!-- --> <!-- --> <script type="application/json" id="__PRIMER_DATA_:R0:__">{"resolvedServerColorMode":"day"}</script></div> </react-partial> <input type="hidden" data-csrf="true" value="39plBx2FPlH6v7WBG81VLfkvYO18evzq1QSUTc/dZuh7AN845M9dwqlqUuT3o/litO77M0kgbQFb/rfeQSynYQ==" /> </div> <div data-view-component="true" class="Layout-sidebar"> <div class="BorderGrid about-margin" data-pjax> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <div class="hide-sm hide-md"> <h2 class="mb-3 h4">About</h2> <p class="f4 my-3"> The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants </p> <div class="my-3 d-flex flex-items-center"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link flex-shrink-0 mr-2"> <path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 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8.477c.285.135.718.273 1.305.273s1.02-.138 1.305-.273L13 6.327Zm-10 0c.285.135.718.273 1.305.273s1.02-.138 1.305-.273L3 6.327Z"></path> </svg> Apache-2.0 license </a> </div> <h3 class="sr-only">Code of conduct</h3> <div class="mt-2"> <a href="#coc-ov-file" class="Link--muted" data-analytics-event="{"category":"Repository Overview","action":"click","label":"location:sidebar;file:code of conduct"}" > <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code-of-conduct mr-2"> <path d="M8.048 2.241c.964-.709 2.079-1.238 3.325-1.241a4.616 4.616 0 0 1 3.282 1.355c.41.408.757.86.996 1.428.238.568.348 1.206.347 1.968 0 2.193-1.505 4.254-3.081 5.862-1.496 1.526-3.213 2.796-4.249 3.563l-.22.163a.749.749 0 0 1-.895 0l-.221-.163c-1.036-.767-2.753-2.037-4.249-3.563C1.51 10.008.007 7.952.002 5.762a4.614 4.614 0 0 1 1.353-3.407C3.123.585 6.223.537 8.048 2.24Zm-1.153.983c-1.25-1.033-3.321-.967-4.48.191a3.115 3.115 0 0 0-.913 2.335c0 1.556 1.109 3.24 2.652 4.813C5.463 11.898 6.96 13.032 8 13.805c.353-.262.758-.565 1.191-.905l-1.326-1.223a.75.75 0 0 1 1.018-1.102l1.48 1.366c.328-.281.659-.577.984-.887L9.99 9.802a.75.75 0 1 1 1.019-1.103l1.384 1.28c.295-.329.566-.661.81-.995L12.92 8.7l-1.167-1.168c-.674-.671-1.78-.664-2.474.03-.268.269-.538.537-.802.797-.893.882-2.319.843-3.185-.032-.346-.35-.693-.697-1.043-1.047a.75.75 0 0 1-.04-1.016c.162-.191.336-.401.52-.623.62-.748 1.356-1.637 2.166-2.417Zm7.112 4.442c.313-.65.491-1.293.491-1.916v-.001c0-.614-.088-1.045-.23-1.385-.143-.339-.357-.633-.673-.949a3.111 3.111 0 0 0-2.218-.915c-1.092.003-2.165.627-3.226 1.602-.823.755-1.554 1.637-2.228 2.45l-.127.154.562.566a.755.755 0 0 0 1.066.02l.794-.79c1.258-1.258 3.312-1.31 4.594-.032.396.394.792.791 1.173 1.173Z"></path> </svg> Code of conduct </a> </div> <include-fragment src="/Ensembl/ensembl-vep/hovercards/citation/sidebar_partial?tree_name=release%2F113"> </include-fragment> <div class="mt-2"> <a href="/Ensembl/ensembl-vep/activity" data-view-component="true" class="Link Link--muted"> <svg text="gray" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-pulse mr-2"> <path d="M6 2c.306 0 .582.187.696.471L10 10.731l1.304-3.26A.751.751 0 0 1 12 7h3.25a.75.75 0 0 1 0 1.5h-2.742l-1.812 4.528a.751.751 0 0 1-1.392 0L6 4.77 4.696 8.03A.75.75 0 0 1 4 8.5H.75a.75.75 0 0 1 0-1.5h2.742l1.812-4.529A.751.751 0 0 1 6 2Z"></path> </svg> <span class="color-fg-muted">Activity</span> </a> </div> <div class="mt-2"> <a href="/Ensembl/ensembl-vep/custom-properties" data-view-component="true" class="Link Link--muted"> <svg text="gray" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-note mr-2"> <path d="M0 3.75C0 2.784.784 2 1.75 2h12.5c.966 0 1.75.784 1.75 1.75v8.5A1.75 1.75 0 0 1 14.25 14H1.75A1.75 1.75 0 0 1 0 12.25Zm1.75-.25a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25v-8.5a.25.25 0 0 0-.25-.25ZM3.5 6.25a.75.75 0 0 1 .75-.75h7a.75.75 0 0 1 0 1.5h-7a.75.75 0 0 1-.75-.75Zm.75 2.25h4a.75.75 0 0 1 0 1.5h-4a.75.75 0 0 1 0-1.5Z"></path> </svg> <span class="color-fg-muted">Custom properties</span> </a> </div> <h3 class="sr-only">Stars</h3> <div class="mt-2"> <a href="/Ensembl/ensembl-vep/stargazers" data-view-component="true" class="Link Link--muted"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-star mr-2"> <path d="M8 .25a.75.75 0 0 1 .673.418l1.882 3.815 4.21.612a.75.75 0 0 1 .416 1.279l-3.046 2.97.719 4.192a.751.751 0 0 1-1.088.791L8 12.347l-3.766 1.98a.75.75 0 0 1-1.088-.79l.72-4.194L.818 6.374a.75.75 0 0 1 .416-1.28l4.21-.611L7.327.668A.75.75 0 0 1 8 .25Zm0 2.445L6.615 5.5a.75.75 0 0 1-.564.41l-3.097.45 2.24 2.184a.75.75 0 0 1 .216.664l-.528 3.084 2.769-1.456a.75.75 0 0 1 .698 0l2.77 1.456-.53-3.084a.75.75 0 0 1 .216-.664l2.24-2.183-3.096-.45a.75.75 0 0 1-.564-.41L8 2.694Z"></path> </svg> <strong>456</strong> stars </a> </div> <h3 class="sr-only">Watchers</h3> <div class="mt-2"> <a href="/Ensembl/ensembl-vep/watchers" data-view-component="true" class="Link Link--muted"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-eye mr-2"> <path d="M8 2c1.981 0 3.671.992 4.933 2.078 1.27 1.091 2.187 2.345 2.637 3.023a1.62 1.62 0 0 1 0 1.798c-.45.678-1.367 1.932-2.637 3.023C11.67 13.008 9.981 14 8 14c-1.981 0-3.671-.992-4.933-2.078C1.797 10.83.88 9.576.43 8.898a1.62 1.62 0 0 1 0-1.798c.45-.677 1.367-1.931 2.637-3.022C4.33 2.992 6.019 2 8 2ZM1.679 7.932a.12.12 0 0 0 0 .136c.411.622 1.241 1.75 2.366 2.717C5.176 11.758 6.527 12.5 8 12.5c1.473 0 2.825-.742 3.955-1.715 1.124-.967 1.954-2.096 2.366-2.717a.12.12 0 0 0 0-.136c-.412-.621-1.242-1.75-2.366-2.717C10.824 4.242 9.473 3.5 8 3.5c-1.473 0-2.825.742-3.955 1.715-1.124.967-1.954 2.096-2.366 2.717ZM8 10a2 2 0 1 1-.001-3.999A2 2 0 0 1 8 10Z"></path> </svg> <strong>30</strong> watching </a> </div> <h3 class="sr-only">Forks</h3> <div class="mt-2"> <a href="/Ensembl/ensembl-vep/forks" data-view-component="true" class="Link Link--muted"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo-forked mr-2"> <path d="M5 5.372v.878c0 .414.336.75.75.75h4.5a.75.75 0 0 0 .75-.75v-.878a2.25 2.25 0 1 1 1.5 0v.878a2.25 2.25 0 0 1-2.25 2.25h-1.5v2.128a2.251 2.251 0 1 1-1.5 0V8.5h-1.5A2.25 2.25 0 0 1 3.5 6.25v-.878a2.25 2.25 0 1 1 1.5 0ZM5 3.25a.75.75 0 1 0-1.5 0 .75.75 0 0 0 1.5 0Zm6.75.75a.75.75 0 1 0 0-1.5.75.75 0 0 0 0 1.5Zm-3 8.75a.75.75 0 1 0-1.5 0 .75.75 0 0 0 1.5 0Z"></path> </svg> <strong>152</strong> forks </a> </div> <div class="mt-2"> <a class="Link--muted" href="/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FEnsembl%2Fensembl-vep&report=Ensembl+%28user%29"> Report repository </a> </div> </div> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame"> <a href="/Ensembl/ensembl-vep/releases" data-view-component="true" class="Link--primary no-underline Link"> Releases <span title="70" data-view-component="true" class="Counter">70</span> </a></h2> <a class="Link--primary d-flex no-underline" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" href="/Ensembl/ensembl-vep/releases/tag/release%2F113.2"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-tag flex-shrink-0 mt-1 color-fg-success"> <path d="M1 7.775V2.75C1 1.784 1.784 1 2.75 1h5.025c.464 0 .91.184 1.238.513l6.25 6.25a1.75 1.75 0 0 1 0 2.474l-5.026 5.026a1.75 1.75 0 0 1-2.474 0l-6.25-6.25A1.752 1.752 0 0 1 1 7.775Zm1.5 0c0 .066.026.13.073.177l6.25 6.25a.25.25 0 0 0 .354 0l5.025-5.025a.25.25 0 0 0 0-.354l-6.25-6.25a.25.25 0 0 0-.177-.073H2.75a.25.25 0 0 0-.25.25ZM6 5a1 1 0 1 1 0 2 1 1 0 0 1 0-2Z"></path> </svg> <div class="ml-2 min-width-0"> <div class="d-flex"> <span class="css-truncate css-truncate-target text-bold mr-2" style="max-width: none;">release/113.2</span> <span title="Label: Latest" data-view-component="true" class="Label Label--success flex-shrink-0"> Latest </span> </div> <div class="text-small color-fg-muted"><relative-time datetime="2024-11-12T14:04:01Z" class="no-wrap">Nov 12, 2024</relative-time></div> </div> </a> <div data-view-component="true" class="mt-3"> <a text="small" data-pjax="#repo-content-pjax-container" data-turbo-frame="repo-content-turbo-frame" href="/Ensembl/ensembl-vep/releases" data-view-component="true" class="Link"> + 69 releases </a></div> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3"> <a href="/orgs/Ensembl/packages?repo_name=ensembl-vep" data-view-component="true" class="Link--primary no-underline Link d-flex flex-items-center"> Packages <span title="0" hidden="hidden" data-view-component="true" class="Counter ml-1">0</span> </a></h2> <div class="text-small color-fg-muted" > No packages published <br> </div> </div> </div> <div class="BorderGrid-row" hidden> <div class="BorderGrid-cell"> <include-fragment src="/Ensembl/ensembl-vep/used_by_list" accept="text/fragment+html"> </include-fragment> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3"> <a href="/Ensembl/ensembl-vep/graphs/contributors" data-view-component="true" class="Link--primary no-underline Link d-flex flex-items-center"> Contributors <span title="27" data-view-component="true" class="Counter ml-1">27</span> </a></h2> <ul class="list-style-none d-flex flex-wrap mb-n2"> <li class="mb-2 mr-2" > <a href="https://github.com/nuno-agostinho" class="" data-hovercard-type="user" data-hovercard-url="/users/nuno-agostinho/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/3199157?s=64&v=4" alt="@nuno-agostinho" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/diegomscoelho" class="" data-hovercard-type="user" data-hovercard-url="/users/diegomscoelho/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/10541523?s=64&v=4" alt="@diegomscoelho" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/nakib103" class="" data-hovercard-type="user" data-hovercard-url="/users/nakib103/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/12125986?s=64&v=4" alt="@nakib103" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/likhitha-surapaneni" class="" data-hovercard-type="user" data-hovercard-url="/users/likhitha-surapaneni/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/10923198?s=64&v=4" alt="@likhitha-surapaneni" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/at7" class="" data-hovercard-type="user" data-hovercard-url="/users/at7/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/4655357?s=64&v=4" alt="@at7" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/aparton" class="" data-hovercard-type="user" data-hovercard-url="/users/aparton/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/33284919?s=64&v=4" alt="@aparton" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/dglemos" class="" data-hovercard-type="user" data-hovercard-url="/users/dglemos/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/44366649?s=64&v=4" alt="@dglemos" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/sarahhunt" class="" data-hovercard-type="user" data-hovercard-url="/users/sarahhunt/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/6123326?s=64&v=4" alt="@sarahhunt" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/ens-lgil" class="" data-hovercard-type="user" data-hovercard-url="/users/ens-lgil/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/6085223?s=64&v=4" alt="@ens-lgil" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/ima23" class="" data-hovercard-type="user" data-hovercard-url="/users/ima23/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/6177217?s=64&v=4" alt="@ima23" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/willmclaren" class="" data-hovercard-type="user" data-hovercard-url="/users/willmclaren/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/1215653?s=64&v=4" alt="@willmclaren" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/helensch" class="" data-hovercard-type="user" data-hovercard-url="/users/helensch/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/25033562?s=64&v=4" alt="@helensch" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/olaaustine" class="" data-hovercard-type="user" data-hovercard-url="/users/olaaustine/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/83219714?s=64&v=4" alt="@olaaustine" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> <li class="mb-2 mr-2" > <a href="https://github.com/jamie-m-a" class="" data-hovercard-type="user" data-hovercard-url="/users/jamie-m-a/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" > <img src="https://avatars.githubusercontent.com/u/50995354?s=64&v=4" alt="@jamie-m-a" size="32" height="32" width="32" data-view-component="true" class="avatar circle" /> </a> </li> </ul> <div data-view-component="true" class="mt-3"> <a text="small" href="/Ensembl/ensembl-vep/graphs/contributors" data-view-component="true" class="Link--inTextBlock Link"> + 13 contributors </a></div> </div> </div> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <h2 class="h4 mb-3">Languages</h2> <div class="mb-2"> <span data-view-component="true" class="Progress"> <span style="background-color:#0298c3 !important;;width: 97.5%;" itemprop="keywords" aria-label="Perl 97.5" data-view-component="true" class="Progress-item color-bg-success-emphasis"></span> <span style="background-color:#ededed !important;;width: 2.5%;" itemprop="keywords" aria-label="Other 2.5" data-view-component="true" class="Progress-item color-bg-success-emphasis"></span> </span></div> <ul class="list-style-none"> <li class="d-inline"> <a class="d-inline-flex flex-items-center flex-nowrap Link--secondary no-underline text-small mr-3" href="/Ensembl/ensembl-vep/search?l=perl" data-ga-click="Repository, language stats search click, location:repo overview"> <svg style="color:#0298c3;" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-dot-fill mr-2"> <path d="M8 4a4 4 0 1 1 0 8 4 4 0 0 1 0-8Z"></path> </svg> <span class="color-fg-default text-bold mr-1">Perl</span> <span>97.5%</span> </a> </li> <li class="d-inline"> <span class="d-inline-flex flex-items-center flex-nowrap text-small mr-3"> <svg style="color:#ededed;" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-dot-fill mr-2"> <path d="M8 4a4 4 0 1 1 0 8 4 4 0 0 1 0-8Z"></path> </svg> <span class="color-fg-default text-bold mr-1">Other</span> <span>2.5%</span> </span> </li> </ul> </div> </div> </div> </div> </div></div> </div> </div> </turbo-frame> </main> </div> </div> <footer class="footer pt-8 pb-6 f6 color-fg-muted p-responsive" role="contentinfo" > <h2 class='sr-only'>Footer</h2> <div class="d-flex flex-justify-center flex-items-center flex-column-reverse flex-lg-row flex-wrap flex-lg-nowrap"> <div class="d-flex flex-items-center flex-shrink-0 mx-2"> <a aria-label="Homepage" title="GitHub" class="footer-octicon mr-2" 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14.082 15H1.918a1.75 1.75 0 0 1-1.543-2.575Zm1.763.707a.25.25 0 0 0-.44 0L1.698 13.132a.25.25 0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path> </svg> <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg> </button> You can’t perform that action at this time. </div> <template id="site-details-dialog"> <details class="details-reset details-overlay details-overlay-dark lh-default color-fg-default hx_rsm" open> <summary role="button" aria-label="Close dialog"></summary> <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal"> <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg> </button> <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> </details-dialog> </details> </template> <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;"> <div class="Popover-message Popover-message--bottom-left Popover-message--large Box color-shadow-large" style="width:360px;"> </div> </div> <template id="snippet-clipboard-copy-button"> <div class="zeroclipboard-container position-absolute right-0 top-0"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn js-clipboard-copy m-2 p-0" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon m-2"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none m-2"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> <template id="snippet-clipboard-copy-button-unpositioned"> <div class="zeroclipboard-container"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn btn-invisible js-clipboard-copy m-2 p-0 d-flex flex-justify-center flex-items-center" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> </div> <div id="js-global-screen-reader-notice" class="sr-only mt-n1" aria-live="polite" aria-atomic="true" ></div> <div id="js-global-screen-reader-notice-assertive" class="sr-only mt-n1" aria-live="assertive" aria-atomic="true"></div> 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