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.
Family Finder: autosomal & X chromosome SNP test
The FTDNA Family Finder test (autosomal & X chromosome) 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. This platform tests 5594 of the 57876 snps in SNPedia.
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 11,300 of these have annotations in SNPedia. 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/
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 BED files and in the form of a BAM file (on request).
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, which Promethease cannot help with without a conversion.
How to download mtDNA fasta file: https://www.familytreedna.com/learn/user-guide/mtdna-myftdna/mt-results-page/
Example Promethease reports for this company
|Platform||Raw data available||Summary|
FTDNA Family Finder
|23andMe v2 & v3, FTDNA Family Finder, Ancestry.com|