{"id":365,"date":"2024-04-25T20:01:12","date_gmt":"2024-04-25T20:01:12","guid":{"rendered":"https:\/\/winterdev.cc\/nwgc-dev\/?page_id=365"},"modified":"2024-09-13T19:17:37","modified_gmt":"2024-09-13T19:17:37","slug":"pipelines","status":"publish","type":"page","link":"https:\/\/nwgc.gs.washington.edu\/wordpress\/tech-platforms\/bioinformatics\/pipelines\/","title":{"rendered":"Pipelines"},"content":{"rendered":"<p><strong>Current pipelines at NWGC:<\/strong><\/p>\n<figure class=\"wp-block-table has-small-font-size\">\n<table class=\"has-dusty-sun-background-color has-background has-fixed-layout\">\n<tbody>\n<tr>\n<td><strong>PIPELINE<\/strong><\/td>\n<td><strong>ALIGNER<\/strong><\/td>\n<td><strong>VARIANT CALLERS<\/strong><\/td>\n<td><strong>DELIVERABLES<\/strong><\/td>\n<\/tr>\n<tr>\n<td><strong>AoU srWGS<\/strong>*<\/td>\n<td>Dragen<\/td>\n<td>Dragen<\/td>\n<td>Annotated VCF, CRAMs<\/td>\n<\/tr>\n<tr>\n<td><strong>AoU LR Ont<\/strong><\/td>\n<td>MM2<\/td>\n<td>Clair3, Sniffles2<\/td>\n<td>VCFs and BAMs<\/td>\n<\/tr>\n<tr>\n<td><strong>AoU LR PB<\/strong><\/td>\n<td>PBMM2<\/td>\n<td>Clair3, PBSV, Sniffles2<\/td>\n<td>VCFs and BAMs<\/td>\n<\/tr>\n<tr>\n<td><strong>TOPMed RNA-Seq<\/strong><\/td>\n<td>STAR<\/td>\n<td>RSEM, RNA-SeqQC<\/td>\n<td>Gene and isoform expression counts, BAMs<\/td>\n<\/tr>\n<tr>\n<td><strong>srWGS, WXS, Custom capture<\/strong><\/td>\n<td>BWA-Mem<\/td>\n<td>GATK<\/td>\n<td>Annotated VCF, CRAMs<\/td>\n<\/tr>\n<\/tbody>\n<\/table><figcaption class=\"wp-element-caption\">* CLIA-validated, Clinical Pipeline<\/figcaption><\/figure>\n<p>All Already Prepared Libraries submitted for sequencing only will be delivered as FASTQs or raw data (BCLs, etc) can be requested for a fee.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Current pipelines at NWGC: PIPELINE ALIGNER VARIANT CALLERS DELIVERABLES AoU srWGS* Dragen Dragen Annotated VCF, CRAMs AoU LR Ont MM2 Clair3, Sniffles2 VCFs and BAMs AoU LR PB PBMM2 Clair3, PBSV, Sniffles2 VCFs and BAMs TOPMed RNA-Seq STAR RSEM, RNA-SeqQC Gene and isoform expression counts, BAMs srWGS, WXS, Custom capture BWA-Mem GATK Annotated VCF, CRAMs * CLIA-validated, Clinical Pipeline All Already Prepared Libraries submitted for sequencing only will be delivered as FASTQs or raw data (BCLs, etc) can be requested&#8230;<\/p>\n<div><a class=\"more-link\" href=\"https:\/\/nwgc.gs.washington.edu\/wordpress\/tech-platforms\/bioinformatics\/pipelines\/\">Continue reading <span class=\"screen-reader-text\">Pipelines<\/span><\/a><\/div>\n","protected":false},"author":2,"featured_media":0,"parent":297,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-365","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/365","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/comments?post=365"}],"version-history":[{"count":1,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/365\/revisions"}],"predecessor-version":[{"id":2389,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/365\/revisions\/2389"}],"up":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/297"}],"wp:attachment":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/media?parent=365"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}