Post 1/4
🚀 Announcing the OpenCRAVAT MCP Server — variant annotation for AI tools via the Model Context Protocol (MCP). Lets LMs/clients call tools so they can fetch authoritative annotations on demand (not from model memory).

Looking for new ways to enrich your variant data? 🔍 We’ve made it simple to browse the OpenCRAVAT ecosystem. From ClinVar and gnomAD to calibrated variant effect predictions and visualization widgets, see what the store has to offer! 🍌 ocstore.opencravat.org #Genomics #VariantAnnotation #BioSky

Discover the latest updates and project status of OpenCRAVAT by exploring the roadmap available on GitHub. Stay informed about the progress and developments by visiting this link: [OpenCRAVAT Roadmap](github.com/orgs/Karchin...). #annotator #opencravat #bioinformatics #opensource #genomics 🧬 🧪 🖥️

Stuck with a three-month VCF backlog? Try these five rapid changes to cut turnaround time in half. (1) prioritize with calibrated predictors; (2) use OpenCRAVAT modular annotators to remove tool fragmentation#annotator #opencravat #bioinformatics #opensource #genomics🧬 🖥️ 🧪

We are planning to launch a new collection of Jupyter notebooks and would love to know if you're interested. If so, please share topics or features you'd like included. Your feedback will help us tailor these notebooks to your needs and preferences.#annotator #opencravat #opensource 🧬 🧪 🖥️

Introducing our latest offering: the Calibrated Classification Package for clinical interpretation of variant effect predictor scores. This innovative package aids users in applying ACMG/AMP variant interpretation guidelines.#annotator #opencravat #bioinformatics #opensource #genomics 🧬 🧪 🖥️

@moezdawood.bsky.social created the AllofUs 250k annotator for OpenCRAVAT to improve genomic research by integrating diverse data, including ancestry-specific allele frequencies. You can read more about Moez's experience developing the annotator here: www.opencravat.org/bringing-gen... #opensource

Help shape the future of genomic variant annotation! We’re looking for community contributors to support OpenCRAVAT — from testing new features to improving documentation and outreach. 📝 Sign up here: forms.gle/v5t2ErBxYzqn... #Genomics #Bioinformatics #OpenScience #Annotation

We are seeking community members interested in taking part in OpenCRAVAT's future. Let us know if you might contribute in any of these areas: Would you be interested in contributing code, bug fixes, or performance improvements? Are there features or issues you’d like to help implement or debug?🧬🖥️

🧪 🧬 Want to explore your own genome? Join our free webinar on how to use OpenCRAVAT to annotate & interpret your personal variants. 📅 July 10 | 🕐 1 PM EDT 🎙️ With Jasmine Baker, PhD & Rachel Karchin, PhD 🔗 tinyurl.com/3ur6vv35 #Genomics #Bioinformatics #OpenSource #OpenCRAVAT🖥️

🧬 Curious about your genome? Join our free webinar on OpenCRAVAT to explore and annotate your own data! 📅 July 10 – 1 PM EDT 🎙️ Baker & Karchin (JHU) 🔗 tinyurl.com/3ur6vv35 #Genomics #Bioinformatics #OpenScience #annotator #opencravat #bioinformatics #opensource #webinar #genomes 🖥🧪

Ever wonder what secrets your personal genome might hold? 🧬 Join us live on July 10 to explore how OpenCRAVAT helps annotate your data & turn it into meaningful insight. Perfect for researchers & curious minds alike. 🔬 Registration link coming soon!🖥

Discover the power of OpenCRAVAT's cutting-edge annotation features that ensure seamless collaboration among users. Its intuitive design makes it easy for everyone to navigate, while enhancing productivity across the board.#annotator #opencravat #bioinformatics #opensource #genomics 🖥️ 🧬

Discover the power of the All of Us annotator with Open Cravat! This tool uses allele frequency data from the All of Us Research Program to explore genetic variations in diverse populations, enhancing precision medicine. Let's innovate healthcare together! #PrecisionMedicine #Genomics #AllOfUs🖥️ 🧬

Introducing the Regeneron Million Exome Annotator curated by Regeneron Genetics Center. Developed with major biobanks and health systems, it provides valuable genetic insights for research. We encourage its use in your research toolkit. #annotator #bioinformatics #opensource #genomics 🧪 🖥️🧬

Need variant annotation fast? OpenCRAVAT makes it easy—whether you're analyzing one variant or thousands. Free, flexible, and built for discovery. Try it today at opencravat.org 🧪🖥🧬

🧬 🖥OpenCRAVAT will integrate the All of Us dataset. That's BILLIONS of gene variation annotations for better understanding our DNA. Check out the blog: www.opencravat.org/opencravat-i... Preprint coming soon from @moezdawood.bsky.social

The cat is out of the bag! We are excited to be a part of this collaboration. Global democratization of deidentified allele count + frequency data with population breakdown from the first ~250k short-read WGS in All of Us designed to plug straight into clinical workflows.🖥️🧪🧬

🖥️ New to OpenCRAVAT? Explore our Vignettes—tutorials designed for easy genomic variant analysis! 🧬 📖 Learn to: ✅ Annotate variants ✅ Interpret results for clinical & research ✅ Utilize powerful analysis tools Start here: karchinlab.github.io/oc_vignettes/ #Genomics #VariantAnnotation #OpenSource

🧬 We Want Your Feedback! 🧬\ Do you use variant annotation software? We’re gathering insights from the genomics community to improve OpenCRAVAT and understand what features matter most to you.💡 Take this quick survey (it takes less than 2 minutes!): https://shorturl.at/iOvMt

Have you seen our updated website? Head over to opencravat.org and check it out! 🖥🧪

Do you have research goals for 2025!? We'd love to hear them! #annotation #OpenCRAVAT #2025 🧪🖥

All OpenCRAVAT systems are back up!

❗We are experiencing a power outage at our data center due to the polar vortex. All OpenCRAVAT systems are currently down. We will update as systems come back online.

Day 12: 🎉 A Genomic Variant Community Our community is at the heart of everything we do. From researchers to clinicians, your feedback shapes OpenCRAVAT's future. Join us in celebrating our shared journey in variant annotation. 💬 Connect with us: https://buff.ly/3ZQ1MZT 🖥️ 🧬 #Community #Genomics

⚙️ Day 11: Widgets That Work for You! Customization is 🔑! OpenCRAVAT’s widgets allow you to visualize variant data in a way that makes sense for your workflow. 🌐 Explore widgets: https://buff.ly/3DbcEbK What’s your favorite widget? #12DaysOfOpenCRAVAT #GenomicTools #Visualization🖥️ 🧬

🧬 New Blog by Dr. Rachel Karchin! Dr. Karchin shares how OpenCRAVAT and CIViC are addressing transparency and interpretability in variant effect predictors. Discover how calibrated predictors are transforming clinical variant classification. 🖥️ 🔗 Read the full post:

🌐 On the 10th day of #OpenCRAVAT, my workflow gave to me… ✨ Powerful API Capabilities! Integrate OpenCRAVAT into pipelines: submit jobs, check statuses, and fetch custom reports programmatically. Explore the API docs: https://buff.ly/4g8lMfP #12DaysofOpenCRAVAT #Genomics

☁️ Day 9 of #OpenCRAVAT: Run on the Cloud! No hardware limits, no delays—just efficient genomic analysis anywhere. Learn how to set up OpenCRAVAT on the cloud today. 🔗Cloud Usage: https://buff.ly/3BjGavq #12DaysofOpenCRAVAT #CloudComputing 🖥️ 🧬 #Genomics #Variants

🔎 Day 8: Eight Data Filtering Options! Refine your results with precision: filter by gene, variant type, pathogenicity score, or population frequency.🧵 #12DaysofOpenCRAVAT #VariantAnalysis 🧬 🖥️

Day 7: Personalize your analysis with OpenCRAVAT! Access numerous annotation tools and refine your focus on certain genes or variants using filters. Automate tasks with Python scripts. Choose input formats.. Export results. Try it locally or in the cloud. #Genomics #VariantAnalysis

🌟 On the 6th day of #OpenCRAVAT, my database gave to me…Six Gene-Level Insights! Which insight is most valuable for your research? CHASMplus, REVEL, PolyPhen-2, @gnomad-project.bsky.social, ClinVar, or COSMIC? Explore OpenCRAVAT at opencravat.org #Genomics #VariantAnalysis #OpenCRAVAT 🧬 🖥️

On the 5th day of #OpenCRAVAT, my platform gave to me… ✨ Five Tips for New Users! New to OpenCRAVAT? Check out the links in this thread. Got questions? Comment below! #12DaysofOpenCRAVAT #Genomics #OpenData #Variants #Annotation

❄️ On the 4th day of #OpenCRAVAT, my workflow gave to me… Four Annotation Sources! Discover how gnomAD4, dbSNP, ClinVar, and COSMIC make your variant analysis powerful. Which do you rely on most? Link to full list of annotators: https://docs.opencravat.org/en/latest/#available-modules

✨ On the 3rd day of #OpenCRAVAT, my tools gave to me… 🎄 Three Custom Report Options! Choose from TXT, Excel, or Sqlite outputs to fit your workflow. Which report type is your favorite? Reply below! 🔗https://buff.ly/3VlpryC 🔗https://buff.ly/4iewYJj #12DaysofOpenCRAVAT #Genomics #VariantAnalysis

🎁 On the 2nd day of #OpenCRAVAT, my software gave to me… ✨ Two New Example Inputs! Test OpenCRAVAT with hgvs and dbsnp inputs. Perfect for trying the software before running your data! 🔗https://buff.ly/3BapIgP & https://buff.ly/49l5yNJ #12DaysofOpenCRAVAT #VariantAnnotation

🎄 On the 1st day of #OpenCRAVAT, my analysis gave to me… ✨ A Single Variant Tool for Free! Quickly annotate any genomic variant right from the new OpenCRAVAT website. Try it now and simplify your workflows! www.opencravat.org run.opencravat.org/webapps/vari...

Starting December 1st, we’re launching the 12 Days of OpenCRAVAT—an adventurer’s guide to mastering genomic variant analysis. Each day, discover powerful tools, tips, and features designed to make your research faster, easier, and more insightful. #12DaysofOpenCRAVAT #Genomics #VariantAnnotation

Exciting news! OpenCRAVAT has a brand-new website AND logo. Check it out at opencravat.org. 🧬 Explore our Single Variant Tool directly on the landing page—annotate a single variant with ease and see how OpenCRAVAT simplifies genomic analysis! 🚀 #Genomics #VariantAnalysis #OpenCRAVAT

Calling all developers! The time is now. Check out our annotator tutorial and create an annotator for your favorite database. open-cravat.readthedocs.io/en/latest/An...

OpenCRAVAT v2.9.0 has landed! 🧬 ✅ Added hgvs and dbsnp example inputs ✅ Better Single Variant Report inputs ✅ Improved input handling with the oc new example-input command #Genomics #OpenCRAVAT #Bioinformatics

Spill the beans briefly – what's the latest and greatest in your research world?

Join our curation session for Increasing the Transparency of Variant Effect Predictors Issue #69 · griffithlab/civic-meeting at the @CG_Consortium Unconference 9am - 5pm CST on Saturday, August 3, 2024 📷Cancer Variant Curation and Coding Unconference - #CGC #variants #Genomics

Now that you have been introduced to OpenCravat, check out our most recent webinar! A tutorial for annotating genomic variants with hands-on demonstrations. youtu.be/yro79-L8Ato?...

Have you seen our new Introduction to OpenCravat video? Head over to our Youtube page! youtu.be/hV6H-3ICKtA?...

Attending #ISMB2024 ? Meet @KarchinRachel and learn about @OpenCRAVAT workflows. Poster 449 July 15 bit.ly/3xVBGtb

The OpenCravat servers will be down July 14-19th for planned maintenance. run.opencravat.org and the module store will be affected. Check our pinned GitHub Issue for more details and updates. github.com/KarchinLab/o...

Please visit us at ISMB 2024! We are poster 449. iscb.junolive.co/ISMB24/live/... #ISMB #Opencravat #Annotator #OpenSource #Genomics

Are you ready for the webinar? Please download OpenCravat to your laptop from: open-cravat.readthedocs.io/en/latest/1.... to follow along during the webinar. Links to data files will also be posted on this discussion thread! github.com/KarchinLab/o...

Are you ready for our webinar with @blkwomencompbio ?? Register and get the pre-webinar details on our github discussion board! github.com/KarchinLab/o...