{"id":1987,"date":"2025-09-25T10:48:09","date_gmt":"2025-09-25T08:48:09","guid":{"rendered":"https:\/\/www.gemma-project.eu\/?page_id=1987"},"modified":"2025-12-16T14:56:24","modified_gmt":"2025-12-16T13:56:24","slug":"gemma-whole-genome-sequencing-data-processing","status":"publish","type":"page","link":"https:\/\/www.gemma-project.eu\/it\/toolbox\/gemma-whole-genome-sequencing-data-processing\/","title":{"rendered":"GEMMA whole genome sequencing data processing"},"content":{"rendered":"<div data-elementor-type=\"wp-page\" data-elementor-id=\"1987\" class=\"elementor elementor-1987\" data-elementor-post-type=\"page\">\n\t\t\t\t<div class=\"elementor-element elementor-element-689e5a76 e-flex e-con-boxed e-con e-parent\" data-id=\"689e5a76\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-2fc5a9ef elementor-widget elementor-widget-heading\" data-id=\"2fc5a9ef\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">GEMMA WHOLE GENOME SEQUENCING DATA PROCESSING<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3ed4e2d4 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"3ed4e2d4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-f5fa609 e-grid e-con-boxed e-con e-parent\" data-id=\"f5fa609\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-740c08b7 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"740c08b7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-cogs\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tTOOL TYPE\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tData analysis, Script\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-124131fe elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"124131fe\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-users\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tTARGET USERS\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tScience &amp; research\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4dcdd0fd elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"4dcdd0fd\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-hands-helping\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tLEAD PARTNER\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tTampere University, CNR-ITB\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-23c43a28 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"23c43a28\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-chart-line\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tCOMPLETENESS\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\t100%\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-69e61903 e-flex e-con-boxed e-con e-parent\" data-id=\"69e61903\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-678ccfe7 elementor-widget elementor-widget-text-editor\" data-id=\"678ccfe7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h4>GEMMA WHOLE GENOME SEQUENCING DATA PROCESSING<\/h4><p>We developed a computational pipeline with accompanying scripts for the alignment for paired end Illumina sequencing data and subsequent variant calling in the GEMMA project.<\/p><ul><li>Alignment: Data is aligned to hg38 reference genome, reads are marked for duplicates and alignment statistics are collected.<\/li><li>Variant calling: Short variants are called and samples are jointly genotyped. The multisample vcf enables downstream analysis such as pca and polygenic risk scores (PRS). Variants are annotated and statistics are collected. Quality control checks sample sex and relatedness for possible sample swaps. De novo variants are detected and inheritance patterns between siblings concordant and discordant for autism are inferred.<\/li><li>CNV calling: CNVs are called and merged to form a multisample vcf. Downstream analysis includes evaluation of CNV distribution between cases and controls as well as pathway analysis.<\/li><\/ul><p>We anticipate releasing the full pipeline and their results together with the anticipated main GEMMA paper.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-3b3f1f21 e-flex e-con-boxed e-con e-parent\" data-id=\"3b3f1f21\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-8657b37 elementor-widget elementor-widget-n-accordion\" data-id=\"8657b37\" data-element_type=\"widget\" data-e-type=\"widget\" data-settings=\"{&quot;default_state&quot;:&quot;expanded&quot;,&quot;max_items_expended&quot;:&quot;one&quot;,&quot;n_accordion_animation_duration&quot;:{&quot;unit&quot;:&quot;ms&quot;,&quot;size&quot;:400,&quot;sizes&quot;:[]}}\" data-widget_type=\"nested-accordion.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"e-n-accordion\" aria-label=\"Accordion. Open links with Enter or Space, close with Escape, and navigate with Arrow Keys\">\n\t\t\t\t\t\t<details id=\"e-n-accordion-item-1400\" class=\"e-n-accordion-item\" open>\n\t\t\t\t<summary class=\"e-n-accordion-item-title\" data-accordion-index=\"1\" tabindex=\"0\" aria-expanded=\"true\" aria-controls=\"e-n-accordion-item-1400\" >\n\t\t\t\t\t<span class='e-n-accordion-item-title-header'><div class=\"e-n-accordion-item-title-text\"> INSTRUCTIONS <\/div><\/span>\n\t\t\t\t\t\t\t<span class='e-n-accordion-item-title-icon'>\n\t\t\t<span class='e-opened' ><i aria-hidden=\"true\" class=\"fas fa-minus\"><\/i><\/span>\n\t\t\t<span class='e-closed'><i aria-hidden=\"true\" class=\"fas fa-plus\"><\/i><\/span>\n\t\t<\/span>\n\n\t\t\t\t\t\t<\/summary>\n\t\t\t\t<div role=\"region\" aria-labelledby=\"e-n-accordion-item-1400\" class=\"elementor-element elementor-element-2f835623 e-con-full e-flex e-con e-child\" data-id=\"2f835623\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-120bf861 elementor-widget elementor-widget-text-editor\" data-id=\"120bf861\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>The scripts are shell scripting appropriate for Linux terminal. Data will be released together with the main GEMMA publication.<\/p><p>Additional instructions:<\/p><p><a href=\"https:\/\/github.com\/karoliinas\/GEMMA_wgs_processing\" target=\"_blank\" rel=\"noopener\">https:\/\/github.com\/karoliinas\/GEMMA_wgs_processing<\/a><\/p><p><a href=\"https:\/\/github.com\/sinithu\/GEMMA_CNV_analysis\" target=\"_blank\" rel=\"noopener\">https:\/\/github.com\/sinithu\/GEMMA_CNV_analysis<\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/details>\n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-4d46407a e-flex e-con-boxed e-con e-parent\" data-id=\"4d46407a\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-751018c7 elementor-widget elementor-widget-heading\" data-id=\"751018c7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">CONTACT<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-560cba9 e-flex e-con-boxed e-con e-parent\" data-id=\"560cba9\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-3d994eb3 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"3d994eb3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-1cbd80e e-flex e-con-boxed e-con e-parent\" data-id=\"1cbd80e\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-18b9706f elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"18b9706f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-list.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul class=\"elementor-icon-list-items\">\n\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<a href=\"http:\/\/karoliina.salenius@tuni.fi\">\n\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-envelope\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Karoliina Salenius<\/span>\n\t\t\t\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<a href=\"http:\/\/sini.thusberg@tuni.fi\">\n\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-envelope\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Sini Thusberg<\/span>\n\t\t\t\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>","protected":false},"excerpt":{"rendered":"<p>GEMMA WHOLE GENOME SEQUENCING DATA PROCESSING TOOL TYPE Data analysis, Script TARGET USERS Science &amp; research LEAD PARTNER Tampere University, CNR-ITB COMPLETENESS 100% GEMMA WHOLE GENOME SEQUENCING DATA PROCESSING We developed a computational pipeline with accompanying scripts for the alignment for paired end Illumina sequencing data and subsequent variant calling in the GEMMA project. Alignment:&hellip;&nbsp;<a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/gemma-whole-genome-sequencing-data-processing\/\" rel=\"bookmark\">Leggi tutto &raquo;<span class=\"screen-reader-text\">GEMMA whole genome sequencing data processing<\/span><\/a><\/p>","protected":false},"author":1,"featured_media":0,"parent":1966,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/template-pagebuilder-full-width.php","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","footnotes":""},"class_list":["post-1987","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1987","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/comments?post=1987"}],"version-history":[{"count":13,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1987\/revisions"}],"predecessor-version":[{"id":2081,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1987\/revisions\/2081"}],"up":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1966"}],"wp:attachment":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/media?parent=1987"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}