mixing hg38 and GRCh38 during variant calling

Question

[yaro]

Hello everyone!

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:

1. GRCh38 genome (NCBI) to align my reads and restricted the alignments to those overlapping with an hg38 exome intervals list;
2. GRCh38 known somatic mutations reference (dbSNP) for base recallibration;
3. hg38 germline variation reference (gnomAD) and hg38 panel of normals (1000 genomes) during the variant calling;
4. GRCh38 annotations

Thanks so much in advance :)

[cmdcolin]

There should not be any difference in coordinate system. There are some interesting differences in some different sources of data but the coordinate system should match up https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

[yaro]

Thanks, @cmdcolin ! That's a relief...