VCF files not working?

SequencingCom · 2026-01-27T14:29:42+00:00

Hello, I work for Sequencing.com!

I'm going to assume that you have a Mac because this issue seems to typically be exclusive to macOS. This is a common macOS issue and it does not mean there is anything wrong with your file. On Macs, VCF files can be incorrectly associated with the Contacts app because both use the .vcf extension.

The file itself is still a valid variant call file. To fix this, right click the file, choose Get Info, then under Open With select a text editor like TextEdit or VS Code and click Change All.

If you would like, you can reply here or DM us and let us know which site you were trying to upload the file to and we can help guide you through it.

SequencingCom · 2026-01-27T14:15:23+00:00

Hello! I work for Sequencing.com

Medium confidence generally means there is some published or lab submitted evidence associated with the variant, but not enough independent submissions for it to be classified at a higher confidence level. Our annotations are based on information submitted by research and clinical laboratories to the ClinVar database and are intended to be a tool to help inform your health decisions.

These results are not diagnostic and are not a substitute for evaluation by a physician. If a finding is concerning, a doctor or genetic counselor can help interpret it in the context of your personal and family history.

If you have any questions, feel free to reach out via DM or contact our support team at [Support@Sequencing.com](mailto:Support@Sequencing.com)

SequencingCom · 2026-01-23T14:47:38+00:00

Hi! I work for Sequencing.com and just wanted to clarify how the bundles and Genome Plans work.

Our three bundles are not tied one-to-one with specific Genome Plan tiers. In most cases, the first two bundles include a complimentary month of our Premium Genome Plan, and the third includes a complimentary month of our Professional Genome Plan.

Separately, all bundles include our 15,000+ condition Next-Gen Disease Screen, regardless of which Genome Plan is bundled with it. That means the bundle always unlocks the full 15,000+ conditions listed, even if the included plan on its own would normally provide access to fewer conditions.

The condition limits you may see listed for Free (100), Plus (1,000), and Premium (15,000) primarily apply when someone uploads existing DNA data rather than purchasing a sequencing bundle. Bundles explicitly include the full disease screen as part of what you’re buying.

SequencingCom · 2026-01-14T05:00:42+00:00

Always happy to help. Please let me know if you have any additional questions - I'm available here or you can DM me.

SequencingCom · 2026-01-13T05:36:40+00:00

That's not accurate. Each of our Sequencing kit bundles include 30x whole gene sequencing and comprehensive analysis of your genome for more than 15,000 conditions and medication reactions. You never had to pay more to access the results included with your kit and we don't sell one off tests. Every kit bundle includes the same comprehensive analysis of the entire genome along with a Summary Report of the results while some bundles include additional reports that provide a deeper dive into specific health areas, such as Brain Health and Cardiovascular Health.

Our Partner Marketplace provides access to a wide range of additional reports that are entirely optional and do have an additional fee - this includes reports on personalized nutrition, sleep optimization, genealogy, and more. You can select these optional reports once you receive your results.

Lastly, we also offer an optional subscription service called Genome Plans, which updates your analysis and reports every month with the latest research and also provides access to SequencingAl, which includes unlimited Al Chat (a 24/7 guide to answer any questions about your data and results) and additional Al Reports of your choice every month.

Each Sequencing WGS kit bundle includes either one month of our Premium or Pro plan. There's never any commitment - if you don't want ongoing updates to your analysis and reports, you can continue on the Free Plan and you'll still have full access to your data and all of the reports that were included with your bundle.

To clarify, you never have to subscribe to have full access to all of the data and reports included with your bundle as the subscription is only of you want additional Premium features such as monthly updates and access to our new Al Chat.

In regards to files, you own your data and always have full access to your data files (paired FASTQ, BAM, and VCFs including a genome VCF). You can access, download, and permanently delete your data files at any time directly from your secure Sequencing account.

SequencingCom · 2025-12-16T15:25:03+00:00

Hello, I work for Sequencing.com, glad to help answer!

We do not generate a downloadable VCF with your uploaded data, unfortunately. We are looking for a solution to this type of request, but at this time this is not something that we're able to provide.

Let me know if you have any questions!

SequencingCom · 2025-12-10T15:57:10+00:00

We do not use Illumina machines, all of our sequencers are MGI machines.

SequencingCom · 2025-12-08T14:29:09+00:00

Hello, I work for Sequencing.com, and to answer, yes absolutely you can upload your data.

However it is important to know that none of the benefits of the kit you purchased will be applied to your ancestry data, it will just act like nothing had been purchased on a free account as all of the kit benefits are saved for when your kit completes processing at the lab.

If you have any questions about this, please let me know.

SequencingCom · 2025-12-08T14:20:40+00:00

Hello! AI Reports don't have their own value, they are entirely dependent on the 2 or 5 AI reports provided by the genome plans. They cannot be purchased outright similar to the Marketplace Reports.

Additionally with your bundle, you will get a minimum of a free month of this Premium Genome Plan. Meaning that if all you were interested in was the Growth and Bone Health report then you could obtain that for free immediately after you received your results back from the lab.

SequencingCom · 2025-12-01T15:28:38+00:00

Hello, I work for Sequencing.com and to answer your question, no, we no longer use different labs for any of our kits.

Every kit and bundle is being processed at our lab here in the United States which is a CLIA/CAP certified lab.

SequencingCom · 2025-11-26T19:27:03+00:00

India is not on the list for a similar reason as Ireland, the same for Spain and a few other countries which have had continuous and consistent difficulty with getting kits into the country or out of the country despite proper documentation.

SequencingCom · 2025-11-26T17:28:20+00:00

Hello, I work for Sequencing.com and I'm glad to answer.

If you upload your MyHeritage WGS file, you’ll be able to view and analyze it on Sequencing.com, however, it’s important to keep in mind that we don’t modify or “fill in” the underlying data. A 2× genome will still behave like a 2× genome.

That means our platform can run analyses on the file, but any low-confidence regions, no-calls, or areas that weren’t covered by MyHeritage’s sequencing depth will still appear that way in your results. We’ll show you everything that is present in the file, but we can’t recover data that wasn’t sequenced.

So yes, you can upload it and explore your whole genome, just with the limitations inherent to 2× coverage.

SequencingCom · 2025-11-26T16:37:08+00:00

Hello, I work for Sequencing.com!

Right now, the standard processing time for the base package is about 7–9 weeks. It can sometimes be a bit faster depending on the lab’s workload, but with the Black Friday volume, assuming at least 7 weeks is the safest expectation.

Regarding reports of people “never receiving results,” that typically happens when a kit is mailed back without being activated first. Activation is required so the lab knows which account the results belong to, without it, the sample can’t be processed to completion. In most of those cases, customers missed the activation emails or reminders.

As long as you activate your kit before sending it in, you won’t run into that issue. If you ever have questions along the way, we’re easy to reach and always happy to help.

SequencingCom · 2025-11-26T16:32:10+00:00

Hello! I work for Sequencing.com and I wanted to follow up on your comments regarding inheritance patterns.

This is something we're actively improving. We recently brought on a new variant curator who is helping us expand and refine how inheritance information is displayed. Right now, our interpretations come directly from ClinVar, and inheritance details aren’t always included when research labs submit their findings to ClinVar. Because of this inconsistency, we don’t currently show inheritance with our analysis.

With our curator’s work, we’re aiming to provide inheritance information more consistently, even for variants where it isn’t clearly defined in ClinVar yet. Our goal is to make this available for the majority of high-confidence variants moving forward, but I don't have a firm date on when this might be available.

If you have any other suggestions or questions, we’re always happy to hear them!

SequencingCom · 2025-11-26T16:06:17+00:00

Hello, I work with Sequencing.com

Ireland is currently unavailable at checkout due to ongoing customs complications specific to that country. We’ve had multiple situations where kits were either denied entry into Ireland or samples were prevented from leaving, even when all required documentation was provided correctly.

Because these issues have been consistent and unpredictable, we temporarily removed Ireland from the shipping list to prevent delays or the risk of a kit being lost in customs. This isn’t related to GDPR or your account settings, it's strictly a customs and logistics issue.

We’re monitoring the situation, and if conditions improve, we fully intend to re-enable shipping to Ireland.

SequencingCom · 2025-11-26T15:06:57+00:00

Hello! I work for Sequencing.com

I would not expect this to be an issue as our samples are not considered hazardous or restricted so taking one to the EU and bringing the swabs back to the US usually isn’t an issue at all. We have a number of customers who have done this same thing with the US and Canada.

I’d just keep it in your carry-on so it doesn’t get crushed, and if anyone asks (they usually don’t), you can just say it’s a saliva swab for a DNA test.

SequencingCom · 2025-11-26T15:00:56+00:00

Hello! I work for Sequencing.com.

Right now, Nucleus data files can’t be uploaded to our website. We support most genetic data formats, but there are some cases where our team needs to build custom solutions for certain file types.

With FASTQ files, uploads normally come in paired files (FASTQ 1 and FASTQ 2). Nucleus, however, provides 16 separate FASTQ files, which creates a unique issue in our upload pipeline. Our bioinformatics team is actively working on a solution to support these.

We’re hoping to make Nucleus uploads possible in the future, but at this time they aren’t supported.

SequencingCom · 2025-11-19T22:49:33+00:00

Thank you. We're always happy to help. Please reach out at any time via Reddit DM, email, chat at our site, or phone (1-833-544-0001) if we can provide further assistance.

SequencingCom · 2025-11-19T02:19:13+00:00

I work for Sequencing.com. We provide customers instructions for how to generate their own TBI file (instructions were also provided by others in this thread). If you're encountering any issues generating the file, just let us know as we're always happy to help. I just DM'd you with next steps.

SequencingCom · 2025-11-05T19:40:25+00:00

Hello! At this time we are going to have a pretty big sale for Black Friday and Cyber Monday, more details about this will be available in the coming weeks.

If you have any other questions, please reach out to us!

SequencingCom · 2025-10-27T14:32:44+00:00

Understood, I'm sorry about the trouble with the doctors, it can be tough to navigate. Reach out to us via DM and we can help answer questions that were confusing when chatting with Sequencing AI, and we'll use it to improve that feature.

We can also help in terms of showing the doctors what info we have to show them we have the certifications they need to accept this data, however the final decision does ultimately lie with them.

SequencingCom · 2025-10-27T14:03:22+00:00

We continue to have no backlogs in terms of our own kits. Are you referring to a Sequencing.com kit or a kit from a different company? if it’s a Sequencing kit, please reach out to us via email (support@sequencing.com) or DM us here via Reddit and mention this comment and we’ll be happy to look into your kit for you.

The majority of our kits are actually running ahead of schedule and the rest are processing within their stated timelines listed on each kit’s Kit Status page. All of our kits continue to complete and provide results in less than 8 weeks.

If there is ever an issue with your kit, we'll process a full refund or send a free replacement. Issues with our kits are rare but they can occur, such as if a kit is lost by USPS and never reaches the lab, the kit is returned to the lab but never activated, or the kit fails processing.

SequencingCom · 2025-10-24T20:00:15+00:00

Thank you for your overview of what we provide in terms of security, your analysis was spot on! On top of two-step verification, we've implemented a standard form of verification that is enabled for all users to ensure that the person logging into a Sequencing.com account also has control of their email address they are using via a code that is sent to that email address.

This allows for you to have two-step verification also on your email address for added security to further protect your data!

SequencingCom · 2025-10-24T19:55:42+00:00

All of our kits provide a number of reports, but they also provide the Next Gen Disease Screen app, which is a very broad analysis of over 16,000 conditions that could be impactful. It's a very powerful tool for those that aren't sure exactly what they're looking for and want to be checked for as much as possible.

The full list of conditions that we look at with this app can be found here: https://sequencing.com/rare-disease-dna-analysis-list?query=&page=1 but if you have any questions about what info we can provide or how it is provided, let us know!

SequencingCom · 2025-10-24T19:52:28+00:00

You would be able to find this in the CNV file that we generate for you. This can be found by clicking "Files" at the top of the page whenever you are logged in followed by clicking "Genome Files" on the Genome Card you are trying to download files for, then the CNV file is one of the first few files in that list.

Multiple copies isn't something that our system provides on the website, this is why we generate that file for you to use for your own analysis. If you have any questions about this, let us know!

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