{"id":8444,"date":"2016-04-18T18:55:36","date_gmt":"2016-04-18T22:55:36","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/?p=8444"},"modified":"2016-05-12T22:52:39","modified_gmt":"2016-05-12T22:52:39","slug":"minor-variant-finder-software-tutorial","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/minor-variant-finder-software-tutorial\/","title":{"rendered":"Minor Variant Finder Software Tutorial"},"content":{"rendered":"<p>You\u2019ve probably heard about the new <a href=\"http:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/sequencing\/sanger-sequencing\/sanger-dna-sequencing\/sanger-sequencing-data-analysis\/minor-variant-finder-software.html?socid=Social_btb\">Minor Variant Finder<\/a> software, and how it will enable 5% somatic variant detection using Sanger sequencing.\u00a0 Give me 5 minutes today, and I will show you how the software works step by step.<\/p>\n<p><iframe loading=\"lazy\" width=\"760\" height=\"428\" src=\"https:\/\/www.youtube.com\/embed\/hMbjhWzRQO8?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p>Minor Variant Finder is perfect for those requiring a cheap, fast, and accurate way to call low frequency variants when working with a small number of targets. It is also a great tool for doing <a href=\"http:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/sequencing\/sanger-sequencing\/next-generation-sequencing-validation.html?socid=Social_btb\">NGS confirmation<\/a> with Sanger sequencing. So how do we get Minor Variant Finder in your lab?<\/p>\n<p>First, visit <a href=\"http:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/sequencing\/sanger-sequencing\/sanger-dna-sequencing\/sanger-sequencing-data-analysis\/minor-variant-finder-software.html?socid=Social_btb\">www.thermofisher.com\/mvf<\/a>.\u00a0 Here, you can download a demo version or purchase the full version. The software installs locally on your computer, and runs in your web browser. Once installation is completed, just click on the icon and your web browser will open automatically. Minor Variant Finder will greet you with all your active projects, allowing you to manage them in one spot.\u00a0 Let\u2019s start a new project.<\/p>\n<p>Here we see the traces view and this is where you import your trace files. After uploading your ab1 files, the software will give you an overview of the quality of your files.\u00a0 Green represents a good quality score and red means a bad score. Double click on the file name and take a closer look at the traces. The quality score is determined by a set of parameters, and you have the option to define those parameters such as signal to noise, trace score, read length and so forth.<\/p>\n<p>This data looks pretty good, so let\u2019s move on to the reference tab. There are two ways to create a reference; one is to use the normal control as a reference, which is the easiest way.\u00a0 The second is to create a reference and\/ or upload an NGS file.<\/p>\n<p>We will use the control for reference here, so let\u2019s just move to the organize tab.<\/p>\n<p>The software compares the forward and reverse traces of your control sample to the forward and reverse traces of your test samples.\u00a0 You can drag your files manually into the control and the test specimen buckets.\u00a0 So first, create an amplicon.\u00a0 Move the controls to the control buckets.\u00a0 Then create a folder for each test specimen.<\/p>\n<p>Another option is the auto-organize function using a naming convention.\u00a0 Click on organize, and tell the software which part of the file name is the amplicon, the specimen, and the control.\u00a0 Click organize, and everything is auto-organized.<\/p>\n<p>Next, go to the Analysis tab, verify that all your data is set up correctly and click on Run Analysis.<\/p>\n<p>And here are your results.\u00a0\u00a0 Here are the reference traces and also the minor variants identified in the test sample files. If you go to the table view, you can see a list of the candidate minor variants, with percentages in both forward and reverse strands. The color here is a review indicator that tells you how much attention you should pay when inspecting these variants. Green means that algorithm has high confidence that it made the right call.\u00a0 Yellow means it should be followed by a visual inspection of the electropherogram.\u00a0 And red means that algorithm is not quite sure, so very critical inspection is needed.<\/p>\n<p>Let\u2019s examine these traces by looking at the electropherogram. Here are the Forward traces and here are reverse traces.\u00a0 This is the control, test sample, and our noise minimized results.\u00a0 The minor variant called is here. Use the slider to adjust the electropherogram for a closer inspection. \u00a0The percentage of both the forward and reverse are on top. And it should be similar for same variant.\u00a0 If all data convinces you that this is a true variant, you can click accept.\u00a0 If you disagree, you can insert a comment. And that\u2019s it for review.<\/p>\n<p>Click on report, and you can generate a variant file of all your findings.<\/p>\n<p>Minor Variant Finder is also a great tool to confirm your NGS results. Check out the <a href=\"http:\/\/tools.thermofisher.com\/content\/sfs\/manuals\/MAN0014835_MinorVariantFinder_v1_UG.pdf?socid=social_btb\">user guide<\/a> on detailed instructions on how to set up a reference, a NGS vcf file for comparison, and how to get a combined report.<\/p>\n<p>And download your copy of Minor Variant Finder at <a href=\"http:\/\/www.thermofisher.com\/mvf\">http:\/\/www.thermofisher.com\/mvf<\/a><\/p>\n<p>Access the full user guide at the link below:\u00a0 <a href=\"http:\/\/tools.thermofisher.com\/content\/sfs\/manuals\/MAN0014835_MinorVariantFinder_v1_UG.pdf?cid=techcomm91c\">http:\/\/tools.thermofisher.com\/content\/sfs\/manuals\/MAN0014835_MinorVariantFinder_v1_UG.pdf?cid=techcomm91c<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>You\u2019ve probably heard about the new Minor Variant Finder software, and how it will enable 5% somatic variant detection using Sanger sequencing.\u00a0 Give me 5 minutes today, and I will show you how the software works step by step. Minor Variant Finder is perfect for those requiring a cheap, fast, and accurate way to call<\/p>\n","protected":false},"author":117,"featured_media":8550,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[184,108,101],"tags":[153,6,25],"division":[],"class_list":["post-8444","post","type-post","status-publish","format-standard","has-post-thumbnail","category-bioinformatics","category-lab-tips-and-tricks","category-product-news","tag-genomic-variants","tag-next-generation-sequencing","tag-sanger-sequencing","entry"],"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.8 (Yoast SEO v27.8) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Minor Variant Finder Software Tutorial - Behind the Bench<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/minor-variant-finder-software-tutorial\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Minor Variant Finder Software Tutorial\" \/>\n<meta property=\"og:description\" content=\"You\u2019ve probably heard about the new Minor Variant Finder software, and how it will enable 5% somatic variant detection using Sanger sequencing.\u00a0 Give me 5 minutes today, and I will show you how the software works step by step. 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Today\u2019s labs are not only looking for accuracy\u2014they need speed, flexibility, and reliable\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"DNA sequencing sample tube with DNA helix and sequencing chromatogram representing Sanger sequencing workflow.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19345,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/precision-oncology-diagnostics\/","url_meta":{"origin":8444,"position":1},"title":"The Expanding Role of Molecular Diagnostics in Precision Oncology","author":"Behind The Bench Staff","date":"January 13, 2026","format":false,"excerpt":"https:\/\/www.youtube.com\/watch?v=F6FfHIizJBY For Dr. Harald Bartsch, a clinical pathologist in southern Bavaria, molecular diagnostic tools have become an indispensable part of his arsenal. \u201cI believe molecular diagnostics play a crucial role in modern oncology, and I see this as the direction everything is headed,\u201d says Dr. Bartsch. While immunohistochemistry remains central\u2026","rel":"","context":"In &quot;Cancer Research&quot;","block_context":{"text":"Cancer Research","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/cancer-research\/"},"img":{"alt_text":"Clinical Pathologist in a Molecular Diagnostics Laboratory","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":19883,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/building-a-better-sample-qc-workflow-from-extraction-to-sequencing\/","url_meta":{"origin":8444,"position":2},"title":"Building a Better Sample QC Workflow: From Extraction to Sequencing","author":"Marlene Gasdia-Cochrane","date":"August 25, 2026","format":false,"excerpt":"Article Summary Successful genomics experiments don't begin with sequencing\u2014they begin with sample quality. Every downstream application, from PCR to next-generation sequencing (NGS), depends on starting with nucleic acids that are accurately quantified and free from contaminants that could compromise results. Establishing a consistent quality control workflow helps laboratories improve reproducibility\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"A pipette drops a liquid into a petri dish with a dna sequence background, science concept. 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A Q&A with Dr. Javier Hernandez Losa, Director of the Molecular Biology Laboratory, Department of Pathology, Hospital Universitario Vall d\u2019Hebron, Barcelona Cancer research increasingly\u2026","rel":"","context":"In &quot;Cancer Research&quot;","block_context":{"text":"Cancer Research","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/cancer-research\/"},"img":{"alt_text":"Dr. Javier Hernandez Losa, Director of the Molecular Biology Laboratory at Hospital Universitario Vall d'Hebron in Barcelona.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Picture133.jpg?resize=1050%2C600&ssl=1 3x"},"classes":[]},{"id":20004,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/a-guide-to-nucleic-acid-quality-control-dna-and-rna-purity\/","url_meta":{"origin":8444,"position":4},"title":"A Guide to Nucleic Acid Quality Control: DNA and RNA Purity","author":"Marlene Gasdia-Cochrane","date":"September 22, 2026","format":false,"excerpt":"Article Summary Nucleic acid quality control helps researchers evaluate DNA and RNA concentration and purity before downstream applications such as PCR, qPCR, and next-generation sequencing (NGS). A standardized workflow combining reliable extraction, concentration and purity assessment, application-appropriate quantification, and consistent laboratory practices can help identify sample issues early, improve reproducibility,\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Close-up shot of a dna sequence on a screen, a digital representation of genetic code, used for analysis.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19976,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/taqman-assay-design-genomic-data\/","url_meta":{"origin":8444,"position":5},"title":"What does it take to keep 20 million Applied Biosystems TaqMan Assays current?","author":"Ashleigh Barlow","date":"September 30, 2026","format":false,"excerpt":"How do you keep more than 20 million TaqMan assays current as genomic knowledge evolves? Every year, our understanding of biology becomes more complete. New variants are discovered, transcript annotations improve, gene models evolve, and our assay-design algorithms advance. That does not mean an assay designed years ago is suddenly\u2026","rel":"","context":"In &quot;Bioinformatics&quot;","block_context":{"text":"Bioinformatics","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/bioinformatics\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/BAN-16090146_1528x860.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/BAN-16090146_1528x860.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/BAN-16090146_1528x860.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/BAN-16090146_1528x860.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/BAN-16090146_1528x860.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/BAN-16090146_1528x860.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/04\/minor-variant.jpg","_links":{"self":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/8444","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/users\/117"}],"replies":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/comments?post=8444"}],"version-history":[{"count":0,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/8444\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media\/8550"}],"wp:attachment":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media?parent=8444"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/categories?post=8444"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/tags?post=8444"},{"taxonomy":"division","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/division?post=8444"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}