Family Tree DNA (FTDNA) is a part of Gene by Gene, Ltd. The Gene By Gene, Ltd, has its own accredited and registered laboratory used by FTDNA and healthcare organizations etc. E.g. FTDNA is National Geographic's partner in their Genographic Project.
FamilyTreeDNA has several types of tests: Y-DNA, mtDNA and autosomal (including X chromosome) tests. Especially the FTDNA autosomal & X chromosome SNP test (Family Finder) data can be used with SNPedia / Promethease.
The .fasta file of mtDNA is not supported by Promethease.
How to download mtDNA fasta file: https://www.familytreedna.com/learn/user-guide/mtdna-myftdna/mt-results-page/
The FTDNA Family Finder test (autosomal & X chromosome SNP test) uses Illumina OmniExpress microarray chip. The chip includes about 696,800 SNPs for autosomal and X (but not Y or mitochondrial) ancestry testing for $99. In chips manufactured on or after December 2012 the number of SNPs on the OmniExpress chip was reduced by Illumina from the original 707,000 SNPs to 696,800.
The chip changed again slightly by the end of 2013, when supplies moved from 12 to 24 samples per chip. FTDNA accepts autosomal raw data transfer from older version of 23andMe (v3) test that was available until end of 2013, as well as AncestryDNA. Getting full access to the transferred results costs $39, without discounts. See FTDNA guide for 23andMe transfer and guide for AncestryDNA transfer.
Family Finder test build 36 raw data file done in March 2014 with the 24 sample chip contained 693,733 autosomal SNP's and 17,691 X-chromosome SNP's for 711,424 total including no-calls and SNP's otherwise not recognized by Promethease. Some 13,193 of these have annotations in SNPedia, though not all SNP's may have been able to be determined in a given sample. FTDNA Family Finder test does not report Y-chromosome and mitochondrial SNP's, and suppresses some other SNP's on the chip. Build 37 files have 27 fewer SNP's listed, likely because they are no longer mapped on it.
How to read Family Finder raw data: https://www.familytreedna.com/learn/autosomal-ancestry/universal-dna-matching/read-family-finder-raw-data-file-2/
How to download Family Finder raw data: https://www.familytreedna.com/learn/autosomal-ancestry/universal-dna-matching/may-download-family-finder-raw-data/
Several different versions of your files are available. The one labeled
- Build 37 Raw Data Concatenated
is the simplest and best choice.
Y-DNA is tested separately, not as a part of Family Finder. The FTDNA BIG Y product launched in autumn 2013 uses next-generation sequencing for the Y-Chromosome. Illumina HiSeq 2000 gives 11,500,000 - 12,500,000 million base-pairs of positions of non-recombining Y-Chromosome. The BIG Y data is available as VCF and in the form of a BAM file (zipped and as a link). The VCF file is accepted by Promethease. The zipped BAM file is not accepted by Promethease.
STR (short tandem repeat) marker tests performed by Family Tree DNA include y-37, y-67, and y-111. These are of no use to Promethease because they are not SNP-based (they are STR tests).
Promethease will not work with the mtDNA FASTA file. mtDNA is tested separately, not as a part of Family Finder. The FTDNA mitochondrial DNA test uses next-generation sequencing technology. mtDNA test raw data is given as a fasta file. We are often asked how to use this with Promethease. We are not aware of any tools for conversion. Even if a suitable one is found or created, the mitochondria is an incredibly small amount of your genome (0.0005%). If you want to use Promethease your best option is to try one of the suggestions at Testing
How to download the mtDNA fasta file: https://www.familytreedna.com/learn/user-guide/mtdna-myftdna/mt-results-page/
Example Promethease reports for this company