I've been working on a variant calling pipeline for WES data and used a mix of hg38 and GRCh38 reference files after reading that hg38 is just an abbreviation of GRCh38, and that they refer to the same thing. But now, I stumbled upon a post mentioning that the two use different coordinates.
I checked the coordinates of my files, and they all seem to agree with each other -- is this a lucky coincidence? Am I risking running into potential issues by mixing hg38 with GRCh38?
More specifically, I used:
- GRCh38 genome (NCBI) to align my reads and restricted the alignments to those overlapping with an hg38 exome intervals list;
- GRCh38 known somatic mutations reference (dbSNP) for base recallibration;
- hg38 germline variation reference (gnomAD) and hg38 panel of normals (1000 genomes) during the variant calling;
- GRCh38 annotations
Thanks so much in advance :)