{"id":541,"date":"2018-07-17T11:13:12","date_gmt":"2018-07-17T09:13:12","guid":{"rendered":"https:\/\/www.personalgenomics.it\/en\/?p=541"},"modified":"2022-07-25T11:15:44","modified_gmt":"2022-07-25T09:15:44","slug":"optimized-pipeline-of-mutect-and-gatk-tools-to-improve-the-detection-of-somatic-single-nucleotide-polymorphisms-in-whole-exome-sequencing-data","status":"publish","type":"post","link":"https:\/\/www.personalgenomics.it\/en\/optimized-pipeline-of-mutect-and-gatk-tools-to-improve-the-detection-of-somatic-single-nucleotide-polymorphisms-in-whole-exome-sequencing-data\/","title":{"rendered":"Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data"},"content":{"rendered":"<div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 fusion-flex-container nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"background-color: rgba(255,255,255,0);background-position: center center;background-repeat: no-repeat;border-width: 0px 0px 0px 0px;border-color:#eae9e9;border-style:solid;\" ><div class=\"fusion-builder-row fusion-row fusion-flex-align-items-flex-start\" style=\"max-width:1352px;margin-left: calc(-4% \/ 2 );margin-right: calc(-4% \/ 2 );\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-flex-column\"><div class=\"fusion-column-wrapper fusion-flex-justify-content-flex-start fusion-content-layout-column\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><style type=\"text\/css\">@media only screen and (max-width:1024px) {.fusion-title.fusion-title-1{margin-top:0px!important; margin-right:0px!important;margin-bottom:15px!important;margin-left:0px!important;}}@media only screen and (max-width:640px) {.fusion-title.fusion-title-1{margin-top:0px!important; margin-right:0px!important;margin-bottom:20px!important; margin-left:0px!important;}}<\/style><div class=\"fusion-title title fusion-title-1 fusion-sep-none fusion-title-text fusion-title-size-three\" style=\"margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;\"><h3 class=\"title-heading-left\" style=\"margin:0;\">Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data<\/h3><\/div><style type=\"text\/css\">@media only screen and (max-width:1024px) {.fusion-title.fusion-title-2{margin-top:0px!important; margin-right:0px!important;margin-bottom:15px!important;margin-left:0px!important;}}@media only screen and (max-width:640px) {.fusion-title.fusion-title-2{margin-top:0px!important; margin-right:0px!important;margin-bottom:20px!important; margin-left:0px!important;}}<\/style><div class=\"fusion-title title fusion-title-2 fusion-sep-none fusion-title-text fusion-title-size-five\" style=\"margin-top:0px;margin-right:0px;margin-bottom:15px;margin-left:0px;\"><h5 class=\"title-heading-left\" style=\"margin:0;\">Detecting somatic mutations for profiling cancer development and chemotherapy resistance.<\/h5><\/div><div class=\"fusion-text fusion-text-1\"><p><em><strong>Authors:<\/strong> do Valle \u00cdF, Giampieri E, Simonetti G, Padella A, Manfrini M, Ferrari A, Papayannidis C, Zironi I, Garonzi M, Bernardi S, Delledonne M, Martinelli G, Remondini D, Castellani G.<\/em><br \/>\nBMC Bioinformatics. 2016 Nov 8;17(Suppl 12):341.<\/p>\n<\/div><div class=\"fusion-text fusion-text-2\"><p>We aimed to develop a pipeline which detects a wide range of single nucleotide mutations with high validation rates. We combined two standard tools \u2013 Genome Analysis Toolkit (GATK) and MuTect \u2013 to create the GATK-LODN method. Experiments in simulated data demonstrated that GATK-LODNincreased both specificity and sensitivity of GATK results. We presented a pipeline that detects a wide range of somatic single nucleotide variants. This pipeline can be helpful in discovery studies aimed to profile the somatic mutational landscape of cancer genomes.<\/p>\n<\/div><div ><style>.fusion-body .fusion-button.button-1{border-radius:8px 8px 8px 8px;}<\/style><a class=\"fusion-button button-flat fusion-button-default-size button-default button-1 fusion-button-default-span fusion-button-default-type\" target=\"_blank\" rel=\"noopener noreferrer\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28185561\"><span class=\"fusion-button-text\">Read more<\/span><\/a><\/div><\/div><style type=\"text\/css\">.fusion-body .fusion-builder-column-0{width:100% !important;margin-top : 0px;margin-bottom : 0px;}.fusion-builder-column-0 > .fusion-column-wrapper {padding-top : 0px !important;padding-right : 0px !important;margin-right : 1.92%;padding-bottom : 0px !important;padding-left : 0px !important;margin-left : 1.92%;}@media only screen and (max-width:1024px) {.fusion-body .fusion-builder-column-0{width:100% !important;}.fusion-builder-column-0 > .fusion-column-wrapper {margin-right : 1.92%;margin-left : 1.92%;}}@media only screen and (max-width:640px) {.fusion-body .fusion-builder-column-0{width:100% !important;}.fusion-builder-column-0 > .fusion-column-wrapper {margin-right : 1.92%;margin-left : 1.92%;}}<\/style><\/div><\/div><style type=\"text\/css\">.fusion-body .fusion-flex-container.fusion-builder-row-1{ padding-top : 0px;margin-top : 0px;padding-right : 0px;padding-bottom : 0px;margin-bottom : 0px;padding-left : 0px;}<\/style><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[19],"tags":[],"_links":{"self":[{"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/posts\/541"}],"collection":[{"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/comments?post=541"}],"version-history":[{"count":3,"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/posts\/541\/revisions"}],"predecessor-version":[{"id":2120,"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/posts\/541\/revisions\/2120"}],"wp:attachment":[{"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/media?parent=541"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/categories?post=541"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.personalgenomics.it\/en\/wp-json\/wp\/v2\/tags?post=541"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}