Realignment to the new T2T (CP086569.2) reference is frequently revealing new unique variants. These new variants help provide more granularity on the Y-Haplotree. But each case is different and there are no guarantees that any new unique variants will be discovered. Realignment works best on whole genome BAM files, although chrY only BAM files will also work.
In any event, the analysis is YFull's responsibility. The Genelach Dáil Cuinn Project assumes no responsibility for the realignment, which is offered on an “as is” basis. We have done the realignment on a few of our own BAM files and everything has proceeded smoothly at YFull. But to emphasize, neither the Genelach Dáil Cuinn Project nor any member individually or severally assumes any responsibility or makes any guarantee or warranty for the realignment. (Lawyers
)Kits that have not been previously analyzed by YFull will first require the normal GRCh38 (hg38) analysis for 45€ and then the subsequent 23€ for the T2T upgrade analysis. Typically this will be for older Dante Labs, FGC, Nebula Genomics, and YSEQ WGS tests that were aligned to the GRCh38 (hg38) reference. As far as we understand currently, YFull is doing the realignment in-house for FTDNA BAM files. They also are including the T2T analysis for new Nebula Genomics WGS tests that transfer directly from Nebula Genomics. But always check with YFull for exact details.
Please PM me here on the Forum for more details.
