You could download the raw sequence reads (FASTQ files) and map them to the new T2T-Y. Probably it makes more sense to wait for a new release of the T2T human g

You could download the raw sequence reads (FASTQ files) and map them to the new T2T-Y. Probably it makes more sense to wait for a new release of the T2T human genome reference, as mapping to a subset of the genome increases false positives. It helps to have some genome bioinformatics knowledge to correctly handle those T2T references.