How Do I Find My Maternal Haplogroup From a Whole-Genome VCF for Free?

Drop any whole-genome VCF or .vcf.gz into the free haplogroup finder. It runs in your browser, never uploads the file, and reports your maternal haplogroup on PhyloTree Build 17 with Haplogrep's scoring. If the VCF carries Y chromosome calls, it also reports a paternal placement.

How do I find my maternal haplogroup from a whole-genome VCF for free?

Open the page and choose your VCF. GRCh37 and GRCh38 both work, and so do plain .vcf and .vcf.gz files. You do not need to convert the file, add rsIDs, or create an account. The file is read on your device. The only genetic data your browser downloads is the two public tree files; nothing from your file is sent anywhere.

A common mistake is converting the VCF to a 23andMe-style file first. You do not need to do that for this question, and converting can drop mitochondrial calls or flatten the data that gives a deep branch.

What the finder actually reports

The maternal result is a branch name, not a percentage and not a medical report. A typical result names the haplogroup or branch, the PhyloTree Build 17 path to it, and a confidence call. If the file has a Y chromosome, the same page reports the paternal haplogroup on the YFull tree, with branch path and, where available, YFull's age estimates. A female sample has no Y chromosome, so the paternal line cannot be read from it.

If your VCF includes mitochondrial variants, the finder walks them down a named tree and stops where the evidence stops. If the VCF has no MT rows or low mitochondrial coverage, the finder may report no maternal placement or stop at a shallower branch.

How the maternal line is scored

Mitochondrial DNA passes from a mother to her children, and it does not recombine like the numbered chromosomes. The mitochondrial genome is short, just 16,569 base pairs. The finder reads only mitochondrial positions, matches them against the defining markers on PhyloTree Build 17, and scores them the way Haplogrep does, without sending any genotype anywhere.

A whole-genome VCF carries nearly all of the mitochondrial variant positions from your sequencing, so the placement can go deep. A consumer chip carries only a few hundred to a few thousand mitochondrial positions and usually stops at a main branch or a few levels below it. Positions a file does not list are not counted as supporting matches. That is why the same person can get a longer haplogroup name from a full mtDNA sequence than from a chip.

Where a VCF lacks the needed positions

A normal whole-genome VCF lists positions where you differ from the reference. If you match the reference at a haplogroup-defining site, that site simply does not appear as a variant. That absence is expected and not a problem. The real gaps to watch for are these:

• No MT or chrM rows at all. Some sequencing pipelines filter out the mitochondrial chromosome.
• Low mitochondrial coverage. Fewer called variants can still place you on a major branch, but deep subbranches may stay uncertain.
• Autosomal-only files. FamilyTreeDNA's Family Finder export is the common example, and the finder will say when no mitochondrial positions are present.

If your VCF has mitochondrial rows but the finder reports none, open the file in a text editor and search for MT or chrM. GRCh38 files often use chrM; GRCh37 files often use MT. The finder accepts both.

Why your result may look different from your testing company's

Different companies use different trees, naming styles, and depths. A longer name is a deeper branch of the same line, not a contradiction. A company might report an older ISOGG-style label while this finder reports the PhyloTree or YFull name for the same branch. The DNA has not changed.

What a haplogroup tells you

It tells you where one of your ancestral lines branches on the human tree and roughly how old that branch is. It does not tell you your health risk, your ancestry percentages, or what to do next. If you want the rest of the VCF interpreted, the free DNA report at HealthOS reads whole-genome VCFs directly for ancestry, traits, medication genes, and both family lines.