Dante Labs VCF Analysis: Which File to Use and How to Read It Free
Dante Labs ships separate SNP and indel VCFs plus huge BAM and FASTQ files. Use the .snp.vcf.gz. Here is why, what to do if tools reject it, and how to read it free.
For Dante Labs whole-genome data, the file to analyze is the one ending in .snp.vcf.gz. Choose it at healthosx.com/dna and your browser reads it on your device, free, into findings on food, medication genes, heart health and traits. Your DNA story needs no account. You don't need the BAM or FASTQ for this: they're tens of gigabytes of raw reads. If the BAM is all you have, the free BAM to VCF converter calls your genotype at about two million known SNPs in your browser and writes a VCF.
The download steps for whole-genome sequencing, on the page itself.
At Dante Labs, the file you want is the one ending .snp.vcf.gz.
The Dante Labs files, explained
A Dante Labs whole genome usually comes with:
- FASTQ files: raw sequencer reads, split across several very large files.
- A BAM file: the reads aligned to the reference genome.
- VCFs: a .snp.vcf.gz (single-letter differences), often an .indel.vcf.gz (small insertions and deletions), and sometimes a structural-variant VCF.
Almost every consumer variant — caffeine, lactose, statins, lipoprotein(a) — is a single-letter SNP, so the SNP VCF is the one to use. The indel file matters for a handful of variants, and no consumer report is built on it.
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.
Why Dante Labs VCFs get rejected
Dante's VCFs are often raw variant-caller output with a dot in the ID column instead of rsIDs. Tools that look variants up by rsID find nothing and either reject the file or show an empty report. You can check in a second: look at the third column of the first data rows. If it's all dots, this is your problem.
On /dna:
- Ancestry works from an rsID-less file on GRCh37, because it matches by position.
- The trait and health report needs rsIDs. Annotate the VCF against dbSNP first, for example with
bcftools annotate, using the same genome build as your file.
Another common failure: a .gz made of several joined compressed sections, which browsers can't read as one stream. If you see that error, unzip the file and choose the plain .vcf.
What you'll see
Every finding opens up: what it means, what to do, and the genotype behind it.
Medication genes, kept behind a tap rather than sprung on you.
The sample genome, read in the browser.
- Food and drink: lactose, caffeine, alcohol, folate, vitamin D, celiac genes, G6PD
- Medications: CYP2C19, CYP2C9, VKORC1, SLCO1B1, TPMT, DPYD, HLA drug-reaction markers
- Heart and inherited risk: lipoprotein(a), iron overload, alpha-1 antitrypsin, LRRK2 G2019S, TTR V122I
- Traits: eyes, hair, freckles, earwax, blood group
| 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.
And if you choose to store the file for Ask your DNA (encrypted, deletable), the chat can go further with a whole genome: haplogroups, polygenic scores, and any variant you name.
Read your Dante Labs SNP VCF free: healthosx.com/dna
New to raw DNA files? Start with the full guide: How to Download & Analyze Your 23andMe Raw Data Free
No raw DNA file yet?
Get a HealthOS DNA Kit: spit in a tube at home, and your ancestry, lineages and traits arrive in your HealthOS account, with the raw file.
See the DNA kitWritten by
HealthOS Research