MyHeritage raw files arrive as CSV rather than tab-separated text, and that small difference is enough to make some tools reject them. Ours does not. A MyHeritage export is a perfectly good input for a qpAdm analysis: the chip covers the ancient panel about as well as the other major array kits, and the file needs no conversion before upload. This guide covers the MyHeritage half of the route, from the download menu to the published model, with one note about MyHeritage's newer low-pass sequencing export that matters for more than qpAdm. If you already have the file, the tiers are on the buying page.
Step one: download the raw file#
In your MyHeritage account, open the DNA menu and choose Manage DNA kits. Each kit has a
three-dots menu on the right; open it and choose Download. MyHeritage asks you to agree to
its terms and confirm by email, and the link in that email hands you a .zip holding a .csv.
Keep the zip as it comes. Our uploader accepts .zip, .gz and the unpacked .csv, and it
recognises the file by its content, so there is nothing to rename or convert.
What the CSV looks like#
A MyHeritage file starts with a block of comment lines describing the kit and the build, then a
header row, then one quoted, comma-separated line per position: the rsID, the chromosome, the
GRCh37 base-pair position and your two alleles joined together, AG for example. Uncalled
positions are written as --.
The chip underneath is an Illumina OmniExpress-derived design of approximately 700k positions, with respectable overlap with the 1240k capture set that most ancient genomes were sequenced against. As always, that figure is approximate and the design has been revised more than once; the only count that matters is the one produced after the merge, and you can measure that for free.
The low-pass WGS export: read this before uploading#
Since 2024 MyHeritage has also sold a low-pass whole-genome sequencing kit, and its export is written in the same CSV shape as the chip file. It behaves differently in one way that matters: the export carries autosomes and the X chromosome only. There are no Y-chromosome rows and no mitochondrial rows.
For qpAdm itself this is harmless, because qpAdm uses the autosomes only; the low-pass export is an acceptable qpAdm input and its autosomal coverage is fine. It does matter for the optional paternal (Y-DNA) and maternal (mtDNA) haplogroup add-ons at checkout, which have nothing to read in that file. If you hold a low-pass MyHeritage export and want a haplogroup, use a different file for that, or skip the add-ons. The free file check below tells you which analyses can read your file, so you will not pay for something the file cannot support.
What to check first: the free file check#
Upload the zip to the free Raw DNA File Check. It detects the format, counts usable markers per chromosome, flags the missing Y and mitochondrial rows if the file is a low-pass export, and returns a coverage verdict for qpAdm: how many of your positions intersect the Allen Ancient DNA Resource (AADR) v66 panel that every paid model is run on. Nothing is ordered and nothing is stored.
That verdict is the honest answer to "will my file work". A valid file with a small overlap will produce standard errors that cannot clear the publish bar, and it is better to know that from a free check than from a report.
What a qpAdm order does with the file#
After you order, your genotypes are converted, filtered of indels and strand-ambiguous positions, and intersected against AADR v66 with Poseidon's trident. The output is a merged sample in which your file and roughly 23,265 reference samples are read at exactly the same positions. From here the vendor is irrelevant; your sample is a target like any other.
An analyst then composes models by hand: a small set of ancient source populations, a set of distant outgroups, and a qpAdm run returning a weight, a standard error and a Z-score per source and one p-value for the whole model. The report publishes all of it for each of two eras, with the complete outgroup list and the full run record. Reading those numbers is set out in How to read qpAdm results.
What changes with coverage: the standard errors#
Every weight's standard error is bounded by the number of positions the model could use, and the merge count of your MyHeritage file fixes that bound. More surviving positions give tighter errors; fewer give wider ones, and no amount of analyst effort can push an error below what the file allows. The publish bar is the same for every file and every tier: p > 0.05, and for every source in every era, |Z| > 3 and a standard error below 0.10. A file that cannot reach it does not get a published model, which the file check tells you in advance.
What does not change: the p-value logic#
Coverage never changes what a p-value means. A passing model is one the data could not refute; a failing one is refuted. That holds for a chip file, a low-pass export and a full-depth VCF alike. Lower coverage makes the test less able to separate close alternatives, which appears as wider errors rather than as a different kind of answer. A breakdown that never fails is a different method entirely; the distinction is drawn in qpAdm vs Global25.
Ordering#
The buying page lists the four tiers, from 29.99 EUR. The publish bar and the report are identical at every tier; a deeper tier buys a longer search past the first model that clears the bar, so that more alternatives have been tried and rejected before one is shown to you. Upload the same zip you ran through the file check, choose the region the model should be scoped to, and the merge starts on our infrastructure. The report is reviewed work and does not render the moment you pay.
If you have a full-depth whole-genome sequence from another provider, a .vcf or .vcf.gz up to
1 GB is accepted instead through the 10 EUR whole-genome upload; a sequencing file usually covers
more of the panel than any chip.
Afterwards: the Model Lab#
Once the report is published, a one-time 10 EUR unlock opens the Model Lab. Your MyHeritage genotypes are already merged into the panel, so you pick sources and outgroups and run your own models, up to 100 per rolling 24 hours. Most will fail; that is what the method is for. You can also download the exact EIGENSTRAT bundle the report was computed from and reproduce everything in ADMIXTOOLS 2 on your own machine. The walkthrough is in Run your own qpAdm models.
To feel a rejection before ordering anything, the free AdmixTools 2 Lab runs real qpAdm over the public reference panel in your browser. It cannot use your sample, but it shows what a failing model looks like, which is the most useful thing to know before reading your own.
A short summary#
- DNA, Manage DNA kits, three dots, Download, confirm by email, keep the zip.
- If it is a low-pass export, remember it has no Y or mitochondrial rows.
- Run the zip through the free file check and read the coverage verdict.
- Order the qpAdm analysis at whichever tier matches how hard you want the search to be.
- Read the report with the p-value, errors and outgroup list in view, then unlock the Model Lab if you want to run the alternatives yourself.
Terms used here are defined in the glossary.
