Using Your Sequencing.com Data Somewhere Else
Your Sequencing.com whole genome is yours to download and use with other tools. Which file to take, how to download it, and how to read it free in your browser.
You can download your Sequencing.com whole-genome data and use it with other tools. Take the VCF (the file ending in .vcf.gz) and choose it at healthosx.com/dna. It's free, your DNA story needs no account, and your browser reads the file on your own device into findings on food, medication genes, heart health and traits.
Sequencing.com has its own app marketplace, and plenty of people are happy there. The usual reasons to take the data elsewhere are a second opinion, apps priced individually, or wanting a reader that doesn't upload the file.
The download steps for whole-genome sequencing, on the page itself.
Unarchive first if the button is there, then take the .vcf.gz.
Which file to take
Sequencing.com typically stores several formats of the same genome:
- VCF (.vcf.gz): the variants. What third-party tools read. Use this.
- BAM or CRAM: aligned reads, tens of gigabytes, for bioinformatics software.
- FASTQ: raw reads, bigger still.
If you uploaded data from another company into Sequencing.com, the original company's file is usually the cleaner one to use.
Typical figures. A chip export far below this was probably cut off; a “raw data” file in the tens of gigabytes is sequencing reads, not variants.
How to download it
- 1.Sign in to your sequencing provider and open its data or downloads section.
- 2.If your files show an Unarchive button, click it and wait until they are ready.
- 3.Download the VCF — the file ending in .vcf.gz (at Dante Labs, the one ending .snp.vcf.gz).
- 4.Upload that .vcf.gz here as it is — no need to unzip it.
- What you get: A variant file ending in .vcf.gz (roughly 100MB–1GB)
- How long: Minutes — or up to 48 hours if your files are archived
Download the VCF, not the FASTQ, BAM or CRAM files. Those are the raw sequencer reads — tens of gigabytes — and the free report reads the VCF. If a BAM is all you have, the free BAM to VCF converter (healthosx.com/dna/convert/bam-to-vcf) calls your genotype at about two million known SNPs in your browser. Some providers’ links expire within a minute, so start the download straight away.
If the file gets rejected
Whole-genome VCFs often have no rsIDs in their ID column (every row shows .). That breaks tools that search by rsID. On /dna, ancestry still works from a GRCh37 file by matching positions; the trait and health report needs rsIDs, which you can add by annotating against dbSNP. Two other things to check are the build (GRCh37 or GRCh38, named in the header lines starting with ##) and whether the download finished. Every rejection reason and its fix.
What you'll see
The short version: what is worth acting on, first.
Ask your DNA: five free questions about your own results.
The sample genome, read in the browser.
The report covers caffeine and lactose, alcohol flush, folate, vitamin D, celiac genes, G6PD, lipoprotein(a), iron overload, alpha-1 antitrypsin, the main medication genes and everyday traits. Every finding shows the genotype and the source.
| What you want | From this file | Why |
|---|---|---|
| Traits, food and drink | Yes | Lactose, caffeine, alcohol flush, bitter taste, vitamin D, folate |
| Medication genes | Yes | CYP2C19, CYP2C9, VKORC1, SLCO1B1, TPMT, DPYD, HLA-B markers |
| CYP2D6 (codeine, tramadol) | No | Needs copy-number calling, which SNP data cannot do |
| Ancestry breakdown | Yes | 15 regions against 157 reference populations, plus the closest of 298 groups and 133 ancient ones |
| Maternal / paternal haplogroup | Partly | A whole genome covers nearly every defining position, so it goes deep |
| Rare disease variants | Partly | Real coverage, but a screen is not a diagnostic test — confirm in an accredited lab |
| Finding relatives | No | Matching needs a database of other people: GEDmatch, MyHeritage, FamilyTreeDNA |
Scroll the table sideways for the rest →
Read on /dna in your browser, except ancestry, which — only if you agree — sends the markers it needs and keeps them with your result until you delete them.
Ancestry (optional) compares your markers with 157 reference populations across 15 regions. Ask your DNA (optional, five free questions) can read a stored whole genome for haplogroups, polygenic scores and any variant you name.
Sequencing.com alternatives for whole-genome VCFs compares the other options.
Why people move their genome
Sequencing.com's model is an app store: your genome sits in your account and you buy apps that read it. That suits some people well. The reasons to also read it elsewhere are practical:
- A second reading of the same genotype. Two tools that agree on a genotype but disagree on its meaning tell you the disagreement is in the interpretation, which is where consumer genetics goes wrong.
- Nothing to upload. A local read means the file doesn't need to sit in another account at all.
- Price. Buying an app per question adds up if you have a handful of questions.
- Portability. Once the VCF is on your own drive, no subscription lapse or company change can take it away.
Keep a copy before anything else
Whole-genome data is the one thing you can't easily replace. Download the VCF, and the BAM or CRAM too if you can spare the space: only the reads let anyone re-call variants later, including the copy-number work a VCF can't support. Store them encrypted, on a drive you'll still have in five years.
FAQ
Can I upload my file back into Sequencing.com later?
Yes. Keeping your own copy doesn't close any doors; it opens the others.
Does /dna need the .tbi index file?
No. Choose the .vcf.gz on its own.
My genome is 4GB. Will my browser cope?
It streams the file in chunks rather than loading it into memory, so size isn't the problem — a few minutes of patience is. It works on a phone, though a laptop is more comfortable.
Take your genome with you. Read your Sequencing.com VCF free: healthosx.com/dna
New to raw DNA files? Start with the full guide: How to Download & Analyze Your 23andMe Raw Data Free
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