Question: Reference genome version between variant calling and annotation
My project is focused on the annotation of human genetic variants (SNPs and short InDels) of WGS and WES.
I am using SNPEff version 5.0. In the snpeff config file I found
- Homo sapiens (hg38) (UCSC).
In contrast, the reference that was used for mapping and variant calling is GCA_000001405.15_GRCh38.
I would like to know if I used one of these two genomes in annotation, could that affect or bias my annotations?
Thanks in advance,
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