hg38 vs GRCh38 chr prefix

Question

[DBScan]

Is there an official documentation about the differences between hg38 and GRCh38? To my understanding, there is no differences between them. However, in gnomAD, which uses GRCh38, SNVs are in the following format: 19-44908822-C-T, without the chr prefix https://gnomad.broadinstitute.org/variant/19-44908822-C-T. Sometimes there is even a discrepancy within the same VCF file, for instance in the high coverage 1000 Genomes dataset (https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/ , where the chromosome names are chr1, whereas the ID is without chr (for instance 22:10519265:CA:C).

Answer 1

[GenoMax]

To my understanding, there is no differences between them.

Primary genome sequence should be identical. There is more in this thread --> Difference between the Fasta files from UCSC and Gencode/Ensembl

UCSC's FAQ page has several questions that would be of interest: https://genome.ucsc.edu/FAQ/FAQgenes.html

Broad's GRCh38 sequences are available from their resource bundle: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle