| Tool | What it contributes | Source |
|---|---|---|
snps |
vendor detection, normalization, build remapping | github.com/apriha/snps |
| yhaplo | Y haplogroup (ISOGG 2016 tree) | github.com/23andMe/yhaplo |
| Haplogrep3 + PhyloTree 17 | mtDNA haplogroup | github.com/genepi/haplogrep3 |
| ClinVar | clinically classified variants at every typed site | ncbi.nlm.nih.gov/clinvar |
| PharmCAT | CPIC/PharmGKB star-allele calling | github.com/PharmGKB/PharmCAT |
| ezancestry | 1000 Genomes population classification | github.com/arvkevi/ezancestry |
| Yleaf | second-opinion Y haplogroup on current YFull / FTDNA / ISOGG trees | github.com/genid/Yleaf |
| rCRS (NC_012920.1) | mitochondrial reference | NCBI |
Evaluated and not used (yet): PLINK 2 (nothing an array file needs that is not already here), ADMIXTURE (needs a multi-GB reference panel), pgsc_calc polygenic scores (arrays need imputation first; planned, see roadmap item 5 in referrals-and-roadmap.md), SNPedia (non-commercial license, no bulk use).
Licenses and credits for everything above: NOTICE.md.
Local: apriha/lineage (shared segments between kits),
PLINK 2, ADMIXTURE + 1000 Genomes, SNPedia.
Web (uploads your data): GEDmatch, James Lick's mthap, Morley's Y-SNP predictor, Promethease, Genetic Genie.